HEADER TRANSFERASE 12-SEP-13 4C5N TITLE STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN TITLE 2 COMPLEX WITH AMP-PCP AND PYRIDOXAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOMETHYLPYRIMIDINE KINASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PYRIDOXAL KINASE; COMPND 5 EC: 2.7.1.35; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: MU50; SOURCE 5 ATCC: 700699; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSFERASE, RIBOKINASE EXPDTA X-RAY DIFFRACTION AUTHOR M.NODWELL,F.ALTE,S.A.SIEBER,S.SCHNEIDER REVDAT 3 20-DEC-23 4C5N 1 REMARK LINK REVDAT 2 16-APR-14 4C5N 1 JRNL REVDAT 1 19-MAR-14 4C5N 0 JRNL AUTH M.B.NODWELL,M.F.KOCH,F.ALTE,S.SCHNEIDER,S.A.SIEBER JRNL TITL A SUBFAMILY OF BACTERIAL RIBOKINASES UTILIZES A JRNL TITL 2 HEMITHIOACETAL FOR PYRIDOXAL PHOSPHATE SALVAGE. JRNL REF J.AM.CHEM.SOC. V. 136 4992 2014 JRNL REFN ISSN 0002-7863 JRNL PMID 24601602 JRNL DOI 10.1021/JA411785R REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 101932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5340 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7254 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.10 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 400 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8109 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 207 REMARK 3 SOLVENT ATOMS : 313 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.67000 REMARK 3 B22 (A**2) : -1.20000 REMARK 3 B33 (A**2) : -0.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.545 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8592 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 8070 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11719 ; 1.938 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18657 ; 0.907 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1100 ; 6.724 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 335 ;37.960 ;26.179 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1423 ;14.456 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;21.804 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1344 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9642 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1788 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4316 ; 1.241 ; 1.404 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4315 ; 1.241 ; 1.404 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5390 ; 1.788 ; 2.095 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4276 ; 2.122 ; 1.708 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 16 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 74 REMARK 3 ORIGIN FOR THE GROUP (A): -18.1375 -4.8867 41.5021 REMARK 3 T TENSOR REMARK 3 T11: 0.1347 T22: 0.0720 REMARK 3 T33: 0.1054 T12: -0.0032 REMARK 3 T13: 0.0691 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 0.9929 L22: 1.4918 REMARK 3 L33: 0.7791 L12: -0.1996 REMARK 3 L13: -0.0301 L23: 0.0204 REMARK 3 S TENSOR REMARK 3 S11: -0.0483 S12: -0.0269 S13: -0.0640 REMARK 3 S21: 0.2357 S22: 0.0091 S23: 0.2106 REMARK 3 S31: -0.0132 S32: -0.0330 S33: 0.0392 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 75 A 167 REMARK 3 ORIGIN FOR THE GROUP (A): -24.3320 -22.0009 41.4476 REMARK 3 T TENSOR REMARK 3 T11: 0.0671 T22: 0.0824 REMARK 3 T33: 0.1595 T12: -0.0339 REMARK 3 T13: 0.0692 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.2970 L22: 3.2200 REMARK 3 L33: 1.2756 L12: 0.0899 REMARK 3 L13: -0.8251 L23: 0.2321 REMARK 3 S TENSOR REMARK 3 S11: -0.0120 S12: -0.1609 S13: -0.1679 REMARK 3 S21: 0.3307 S22: -0.0539 S23: 0.1975 REMARK 3 S31: 0.0671 S32: 0.0599 S33: 0.0659 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 168 A 199 REMARK 3 ORIGIN FOR THE GROUP (A): -19.5752 -28.2144 28.9042 REMARK 3 T TENSOR REMARK 3 T11: 0.0769 T22: 0.0595 REMARK 3 T33: 0.1865 T12: -0.0228 REMARK 3 T13: 0.0480 T23: -0.0560 REMARK 3 L TENSOR REMARK 3 L11: 6.1464 L22: 4.4479 REMARK 3 L33: 2.2092 L12: 0.9916 REMARK 3 L13: -1.5791 L23: -0.0824 REMARK 3 S TENSOR REMARK 3 S11: -0.2341 S12: 0.0051 S13: -0.3169 REMARK 3 S21: -0.2603 S22: 0.0427 S23: -0.0646 REMARK 3 S31: 0.1660 S32: 0.0750 S33: 0.1914 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 200 A 276 REMARK 3 ORIGIN FOR THE GROUP (A): -11.5644 -15.5342 26.5300 REMARK 3 T TENSOR REMARK 3 T11: 0.0642 T22: 0.0785 REMARK 3 T33: 0.0949 T12: -0.0085 REMARK 3 T13: 0.0333 T23: -0.0265 REMARK 3 L TENSOR REMARK 3 L11: 1.1251 L22: 1.5296 REMARK 3 L33: 0.6772 L12: -0.0662 REMARK 3 L13: -0.4717 L23: -0.1560 REMARK 3 S TENSOR REMARK 3 S11: -0.0785 S12: 0.1352 S13: -0.1849 REMARK 3 S21: -0.0610 S22: 0.0113 S23: 0.0347 REMARK 3 S31: 0.1182 S32: 0.0160 S33: 0.0672 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 96 REMARK 3 ORIGIN FOR THE GROUP (A): -24.8668 -5.7421 0.4538 REMARK 3 T TENSOR REMARK 3 T11: 0.1142 T22: 0.0846 REMARK 3 T33: 0.0829 T12: -0.0107 REMARK 3 T13: -0.0020 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 1.0040 L22: 1.2328 REMARK 3 L33: 1.0227 L12: 0.1128 REMARK 3 L13: -0.1691 L23: 0.1970 REMARK 3 S TENSOR REMARK 3 S11: 0.0080 S12: -0.1127 S13: -0.0669 REMARK 3 S21: 0.1812 S22: -0.0345 S23: 0.0835 REMARK 3 S31: 0.0517 S32: -0.0049 S33: 0.0266 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 97 B 167 REMARK 3 ORIGIN FOR THE GROUP (A): -27.4841 -24.0786 -0.6342 REMARK 3 T TENSOR REMARK 3 T11: 0.1161 T22: 0.0807 REMARK 3 T33: 0.1086 T12: -0.0062 REMARK 3 T13: 0.0123 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 1.2445 L22: 3.4462 REMARK 3 L33: 1.5411 L12: -0.4175 REMARK 3 L13: -0.4785 L23: 0.0384 REMARK 3 S TENSOR REMARK 3 S11: -0.0518 S12: -0.2291 S13: -0.1753 REMARK 3 S21: 0.4212 S22: -0.0363 S23: 0.1257 REMARK 3 S31: 0.1428 S32: 0.1699 S33: 0.0881 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 168 B 183 REMARK 3 ORIGIN FOR THE GROUP (A): -23.6229 -26.3387 -7.6242 REMARK 3 T TENSOR REMARK 3 T11: 0.1476 T22: 0.0869 REMARK 3 T33: 0.0857 T12: 0.0287 REMARK 3 T13: -0.0460 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 8.1545 L22: 5.4007 REMARK 3 L33: 3.3008 L12: -1.6944 REMARK 3 L13: -1.4846 L23: 0.1043 REMARK 3 S TENSOR REMARK 3 S11: 0.2365 S12: -0.0329 S13: -0.1047 REMARK 3 S21: -0.0674 S22: -0.1995 S23: -0.2328 REMARK 3 S31: 0.4508 S32: 0.4045 S33: -0.0369 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 184 B 276 REMARK 3 ORIGIN FOR THE GROUP (A): -18.4273 -18.0308 -14.9715 REMARK 3 T TENSOR REMARK 3 T11: 0.1206 T22: 0.0790 REMARK 3 T33: 0.0808 T12: 0.0172 REMARK 3 T13: 0.0103 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 1.0925 L22: 1.5057 REMARK 3 L33: 0.2106 L12: 0.4881 REMARK 3 L13: 0.1216 L23: 0.0294 REMARK 3 S TENSOR REMARK 3 S11: 0.0251 S12: 0.0965 S13: -0.1342 REMARK 3 S21: -0.1134 S22: -0.0551 S23: -0.1010 REMARK 3 S31: 0.1336 S32: 0.0534 S33: 0.0300 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 86 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6659 5.5109 -0.0300 REMARK 3 T TENSOR REMARK 3 T11: 0.0849 T22: 0.0931 REMARK 3 T33: 0.0642 T12: -0.0070 REMARK 3 T13: -0.0168 T23: -0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.6630 L22: 0.8260 REMARK 3 L33: 0.6536 L12: 0.1989 REMARK 3 L13: -0.0879 L23: -0.1258 REMARK 3 S TENSOR REMARK 3 S11: 0.0327 S12: -0.0927 S13: 0.0181 REMARK 3 S21: 0.1067 S22: -0.0503 S23: -0.0200 REMARK 3 S31: -0.0322 S32: 0.0472 S33: 0.0176 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 87 C 137 REMARK 3 ORIGIN FOR THE GROUP (A): -7.6911 16.8638 0.6555 REMARK 3 T TENSOR REMARK 3 T11: 0.0822 T22: 0.1135 REMARK 3 T33: 0.0669 T12: -0.0590 REMARK 3 T13: -0.0313 T23: 0.0189 REMARK 3 L TENSOR REMARK 3 L11: 2.1478 L22: 2.1986 REMARK 3 L33: 3.0941 L12: -0.0237 REMARK 3 L13: 0.1398 L23: -0.0288 REMARK 3 S TENSOR REMARK 3 S11: 0.0243 S12: -0.2432 S13: -0.0420 REMARK 3 S21: 0.1826 S22: -0.0481 S23: -0.0635 REMARK 3 S31: -0.2459 S32: 0.0914 S33: 0.0238 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 138 C 203 REMARK 3 ORIGIN FOR THE GROUP (A): -15.9907 28.5743 -10.8112 REMARK 3 T TENSOR REMARK 3 T11: 0.0764 T22: 0.0532 REMARK 3 T33: 0.0796 T12: -0.0224 REMARK 3 T13: -0.0201 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 1.8832 L22: 1.5052 REMARK 3 L33: 2.1846 L12: 0.1907 REMARK 3 L13: 1.2511 L23: 0.0593 REMARK 3 S TENSOR REMARK 3 S11: -0.0553 S12: -0.0743 S13: 0.1805 REMARK 3 S21: -0.1621 S22: -0.0412 S23: 0.0116 REMARK 3 S31: -0.1862 S32: -0.0463 S33: 0.0965 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 204 C 276 REMARK 3 ORIGIN FOR THE GROUP (A): -22.1383 13.6593 -16.4299 REMARK 3 T TENSOR REMARK 3 T11: 0.1072 T22: 0.0778 REMARK 3 T33: 0.0536 T12: -0.0036 REMARK 3 T13: -0.0244 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.3771 L22: 1.4596 REMARK 3 L33: 0.8644 L12: 0.2970 REMARK 3 L13: 0.2808 L23: -0.2309 REMARK 3 S TENSOR REMARK 3 S11: -0.0199 S12: 0.0529 S13: 0.0575 REMARK 3 S21: -0.1447 S22: -0.0009 S23: 0.0678 REMARK 3 S31: -0.0816 S32: -0.0087 S33: 0.0208 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 88 REMARK 3 ORIGIN FOR THE GROUP (A): -11.8098 4.6309 42.7831 REMARK 3 T TENSOR REMARK 3 T11: 0.1428 T22: 0.0647 REMARK 3 T33: 0.0531 T12: -0.0015 REMARK 3 T13: 0.0233 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.7068 L22: 1.6183 REMARK 3 L33: 0.6174 L12: 0.4576 REMARK 3 L13: -0.1654 L23: -0.1907 REMARK 3 S TENSOR REMARK 3 S11: -0.0074 S12: -0.0472 S13: 0.0378 REMARK 3 S21: 0.2640 S22: -0.0264 S23: 0.0497 REMARK 3 S31: -0.0668 S32: 0.0373 S33: 0.0338 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 89 D 156 REMARK 3 ORIGIN FOR THE GROUP (A): -6.9055 19.8244 42.4444 REMARK 3 T TENSOR REMARK 3 T11: 0.1509 T22: 0.1163 REMARK 3 T33: 0.0677 T12: -0.0440 REMARK 3 T13: 0.0222 T23: -0.0000 REMARK 3 L TENSOR REMARK 3 L11: 1.3256 L22: 3.3947 REMARK 3 L33: 1.2969 L12: -0.2523 REMARK 3 L13: 0.4649 L23: -0.1128 REMARK 3 S TENSOR REMARK 3 S11: 0.0083 S12: -0.1317 S13: 0.0643 REMARK 3 S21: 0.4011 S22: -0.0488 S23: 0.0490 REMARK 3 S31: -0.0216 S32: -0.0956 S33: 0.0406 REMARK 3 REMARK 3 TLS GROUP : 15 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 157 D 194 REMARK 3 ORIGIN FOR THE GROUP (A): -9.1335 27.6474 32.6039 REMARK 3 T TENSOR REMARK 3 T11: 0.1132 T22: 0.1055 REMARK 3 T33: 0.0799 T12: -0.0128 REMARK 3 T13: 0.0432 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 3.4374 L22: 2.6296 REMARK 3 L33: 1.6690 L12: -0.0198 REMARK 3 L13: 0.4469 L23: 0.2228 REMARK 3 S TENSOR REMARK 3 S11: -0.0017 S12: 0.0355 S13: 0.1928 REMARK 3 S21: 0.0604 S22: -0.0422 S23: 0.0976 REMARK 3 S31: -0.0754 S32: -0.0681 S33: 0.0439 REMARK 3 REMARK 3 TLS GROUP : 16 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 195 D 276 REMARK 3 ORIGIN FOR THE GROUP (A): -15.9262 14.8869 26.1869 REMARK 3 T TENSOR REMARK 3 T11: 0.1105 T22: 0.0923 REMARK 3 T33: 0.0562 T12: -0.0288 REMARK 3 T13: 0.0005 T23: 0.0098 REMARK 3 L TENSOR REMARK 3 L11: 0.9213 L22: 2.0190 REMARK 3 L33: 0.3773 L12: 0.2915 REMARK 3 L13: 0.1564 L23: -0.0408 REMARK 3 S TENSOR REMARK 3 S11: -0.0297 S12: 0.0069 S13: 0.0432 REMARK 3 S21: -0.1024 S22: 0.0193 S23: 0.1979 REMARK 3 S31: -0.0511 S32: -0.0661 S33: 0.0104 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4C5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1290058337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 107272 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 48.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4C5J REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM HEPES PH7.6, 2M NH4SO4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 31.09500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.10500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 84.10500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.09500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.33000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 VAL A 109 REMARK 465 CYS A 110 REMARK 465 LYS A 111 REMARK 465 GLY A 112 REMARK 465 GLU A 113 REMARK 465 ASP A 114 REMARK 465 GLU A 115 REMARK 465 VAL A 116 REMARK 465 CYS B 110 REMARK 465 LYS B 111 REMARK 465 GLY B 112 REMARK 465 GLU B 113 REMARK 465 ASP B 114 REMARK 465 GLU B 115 REMARK 465 VAL B 116 REMARK 465 GLY C 1 REMARK 465 VAL C 109 REMARK 465 CYS C 110 REMARK 465 LYS C 111 REMARK 465 GLY C 112 REMARK 465 GLU C 113 REMARK 465 ASP C 114 REMARK 465 GLU C 115 REMARK 465 VAL C 116 REMARK 465 LEU C 117 REMARK 465 LYS D 111 REMARK 465 GLY D 112 REMARK 465 GLU D 113 REMARK 465 ASP D 114 REMARK 465 GLU D 115 REMARK 465 VAL D 116 REMARK 465 LEU D 117 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 160 NZ REMARK 470 LYS A 179 CG CD CE NZ REMARK 470 GLN A 183 CD OE1 NE2 REMARK 470 LEU B 117 CG CD1 CD2 REMARK 470 LYS B 151 CG CD CE NZ REMARK 470 LYS B 179 CE NZ REMARK 470 LYS D 179 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN D 118 N GLY D 120 1.90 REMARK 500 OD2 ASP A 259 O HOH A 2067 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP B 270 O ASN D 118 2454 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR C 94 CE1 TYR C 94 CZ -0.102 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B 59 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP B 167 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG C 89 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP D 270 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 18 -169.97 -122.81 REMARK 500 THR A 137 56.05 -117.74 REMARK 500 LEU A 181 -71.45 -123.74 REMARK 500 GLU A 267 148.63 -171.55 REMARK 500 ALA B 18 -165.63 -124.46 REMARK 500 ASN B 153 18.85 -141.45 REMARK 500 GLN B 194 -45.24 -136.85 REMARK 500 ALA C 18 -165.25 -115.00 REMARK 500 ASN C 252 -161.74 -161.98 REMARK 500 ALA D 16 11.27 82.64 REMARK 500 ALA D 18 -160.20 -122.99 REMARK 500 PRO D 119 6.77 -18.01 REMARK 500 TYR D 208 79.31 -119.17 REMARK 500 ILE D 266 -65.29 -109.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXL B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXL C 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP C 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UEG D 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP D 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1278 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 1279 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1277 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1278 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1278 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C5J RELATED DB: PDB REMARK 900 STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS REMARK 900 RELATED ID: 4C5K RELATED DB: PDB REMARK 900 STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN REMARK 900 COMPLEX WITH ADP REMARK 900 RELATED ID: 4C5L RELATED DB: PDB REMARK 900 STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN REMARK 900 COMPLEX WITH PYRIDOXAL REMARK 900 RELATED ID: 4C5M RELATED DB: PDB REMARK 900 STRUCTURE OF THE PYRIDOXAL KINASE FROM STAPHYLOCOCCUS AUREUS IN REMARK 900 COMPLEX WITH AMP-PCP REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST AMINOACID IS A GLY INSTEAD OF MET DUE TO REMOVAL OF REMARK 999 THE AFFINITY TAG DBREF 4C5N A 1 276 UNP C8MK44 C8MK44_STAAU 1 276 DBREF 4C5N B 1 276 UNP C8MK44 C8MK44_STAAU 1 276 DBREF 4C5N C 1 276 UNP C8MK44 C8MK44_STAAU 1 276 DBREF 4C5N D 1 276 UNP C8MK44 C8MK44_STAAU 1 276 SEQRES 1 A 276 GLY ALA LEU LYS LYS VAL LEU THR ILE ALA GLY SER ASP SEQRES 2 A 276 THR SER ALA GLY ALA GLY MET GLN ALA ASP LEU LYS THR SEQRES 3 A 276 PHE GLN GLU LEU ASP THR TYR GLY MET VAL ALA LEU THR SEQRES 4 A 276 ALA ILE VAL THR MET ASP LYS ASP THR TRP SER HIS ASP SEQRES 5 A 276 VAL THR PRO LEU PRO MET ASP VAL PHE GLU LYS GLN LEU SEQRES 6 A 276 GLU THR ALA LEU SER ILE GLY PRO ASP ALA ILE LYS THR SEQRES 7 A 276 GLY MET LEU GLY THR GLU GLU ILE ILE LYS ARG ALA GLY SEQRES 8 A 276 GLU VAL TYR GLU ALA SER ASN ALA GLN TYR PHE VAL VAL SEQRES 9 A 276 ASP PRO VAL MET VAL CYS LYS GLY GLU ASP GLU VAL LEU SEQRES 10 A 276 ASN PRO GLY ASN THR GLU ALA MET ILE LYS TYR LEU LEU SEQRES 11 A 276 PRO LYS ALA THR VAL VAL THR PRO ASN LEU PHE GLU ALA SEQRES 12 A 276 GLY GLN LEU SER GLY LEU GLY LYS LEU ASN SER ILE GLU SEQRES 13 A 276 ASP MET LYS LYS ALA ALA THR ILE ILE PHE ASP LYS GLY SEQRES 14 A 276 ALA GLN HIS VAL ILE ILE LYS GLY GLY LYS ALA LEU ASP SEQRES 15 A 276 GLN ASP LYS SER TYR ASP LEU TYR TYR ASP GLY GLN THR SEQRES 16 A 276 PHE TYR GLN LEU THR THR ASP MET PHE GLN GLN SER TYR SEQRES 17 A 276 ASN HIS GLY ALA GLY CYS THR PHE ALA ALA ALA THR THR SEQRES 18 A 276 ALA TYR LEU ALA ASN GLY LYS SER PRO LYS GLU ALA VAL SEQRES 19 A 276 ILE SER ALA LYS ALA PHE VAL ALA SER ALA ILE LYS ASN SEQRES 20 A 276 GLY TRP LYS MET ASN ASP PHE VAL GLY PRO VAL ASP HIS SEQRES 21 A 276 GLY ALA TYR ASN ARG ILE GLU HIS ILE ASP VAL GLU VAL SEQRES 22 A 276 THR GLU VAL SEQRES 1 B 276 GLY ALA LEU LYS LYS VAL LEU THR ILE ALA GLY SER ASP SEQRES 2 B 276 THR SER ALA GLY ALA GLY MET GLN ALA ASP LEU LYS THR SEQRES 3 B 276 PHE GLN GLU LEU ASP THR TYR GLY MET VAL ALA LEU THR SEQRES 4 B 276 ALA ILE VAL THR MET ASP LYS ASP THR TRP SER HIS ASP SEQRES 5 B 276 VAL THR PRO LEU PRO MET ASP VAL PHE GLU LYS GLN LEU SEQRES 6 B 276 GLU THR ALA LEU SER ILE GLY PRO ASP ALA ILE LYS THR SEQRES 7 B 276 GLY MET LEU GLY THR GLU GLU ILE ILE LYS ARG ALA GLY SEQRES 8 B 276 GLU VAL TYR GLU ALA SER ASN ALA GLN TYR PHE VAL VAL SEQRES 9 B 276 ASP PRO VAL MET VAL CYS LYS GLY GLU ASP GLU VAL LEU SEQRES 10 B 276 ASN PRO GLY ASN THR GLU ALA MET ILE LYS TYR LEU LEU SEQRES 11 B 276 PRO LYS ALA THR VAL VAL THR PRO ASN LEU PHE GLU ALA SEQRES 12 B 276 GLY GLN LEU SER GLY LEU GLY LYS LEU ASN SER ILE GLU SEQRES 13 B 276 ASP MET LYS LYS ALA ALA THR ILE ILE PHE ASP LYS GLY SEQRES 14 B 276 ALA GLN HIS VAL ILE ILE LYS GLY GLY LYS ALA LEU ASP SEQRES 15 B 276 GLN ASP LYS SER TYR ASP LEU TYR TYR ASP GLY GLN THR SEQRES 16 B 276 PHE TYR GLN LEU THR THR ASP MET PHE GLN GLN SER TYR SEQRES 17 B 276 ASN HIS GLY ALA GLY CYS THR PHE ALA ALA ALA THR THR SEQRES 18 B 276 ALA TYR LEU ALA ASN GLY LYS SER PRO LYS GLU ALA VAL SEQRES 19 B 276 ILE SER ALA LYS ALA PHE VAL ALA SER ALA ILE LYS ASN SEQRES 20 B 276 GLY TRP LYS MET ASN ASP PHE VAL GLY PRO VAL ASP HIS SEQRES 21 B 276 GLY ALA TYR ASN ARG ILE GLU HIS ILE ASP VAL GLU VAL SEQRES 22 B 276 THR GLU VAL SEQRES 1 C 276 GLY ALA LEU LYS LYS VAL LEU THR ILE ALA GLY SER ASP SEQRES 2 C 276 THR SER ALA GLY ALA GLY MET GLN ALA ASP LEU LYS THR SEQRES 3 C 276 PHE GLN GLU LEU ASP THR TYR GLY MET VAL ALA LEU THR SEQRES 4 C 276 ALA ILE VAL THR MET ASP LYS ASP THR TRP SER HIS ASP SEQRES 5 C 276 VAL THR PRO LEU PRO MET ASP VAL PHE GLU LYS GLN LEU SEQRES 6 C 276 GLU THR ALA LEU SER ILE GLY PRO ASP ALA ILE LYS THR SEQRES 7 C 276 GLY MET LEU GLY THR GLU GLU ILE ILE LYS ARG ALA GLY SEQRES 8 C 276 GLU VAL TYR GLU ALA SER ASN ALA GLN TYR PHE VAL VAL SEQRES 9 C 276 ASP PRO VAL MET VAL CYS LYS GLY GLU ASP GLU VAL LEU SEQRES 10 C 276 ASN PRO GLY ASN THR GLU ALA MET ILE LYS TYR LEU LEU SEQRES 11 C 276 PRO LYS ALA THR VAL VAL THR PRO ASN LEU PHE GLU ALA SEQRES 12 C 276 GLY GLN LEU SER GLY LEU GLY LYS LEU ASN SER ILE GLU SEQRES 13 C 276 ASP MET LYS LYS ALA ALA THR ILE ILE PHE ASP LYS GLY SEQRES 14 C 276 ALA GLN HIS VAL ILE ILE LYS GLY GLY LYS ALA LEU ASP SEQRES 15 C 276 GLN ASP LYS SER TYR ASP LEU TYR TYR ASP GLY GLN THR SEQRES 16 C 276 PHE TYR GLN LEU THR THR ASP MET PHE GLN GLN SER TYR SEQRES 17 C 276 ASN HIS GLY ALA GLY CYS THR PHE ALA ALA ALA THR THR SEQRES 18 C 276 ALA TYR LEU ALA ASN GLY LYS SER PRO LYS GLU ALA VAL SEQRES 19 C 276 ILE SER ALA LYS ALA PHE VAL ALA SER ALA ILE LYS ASN SEQRES 20 C 276 GLY TRP LYS MET ASN ASP PHE VAL GLY PRO VAL ASP HIS SEQRES 21 C 276 GLY ALA TYR ASN ARG ILE GLU HIS ILE ASP VAL GLU VAL SEQRES 22 C 276 THR GLU VAL SEQRES 1 D 276 GLY ALA LEU LYS LYS VAL LEU THR ILE ALA GLY SER ASP SEQRES 2 D 276 THR SER ALA GLY ALA GLY MET GLN ALA ASP LEU LYS THR SEQRES 3 D 276 PHE GLN GLU LEU ASP THR TYR GLY MET VAL ALA LEU THR SEQRES 4 D 276 ALA ILE VAL THR MET ASP LYS ASP THR TRP SER HIS ASP SEQRES 5 D 276 VAL THR PRO LEU PRO MET ASP VAL PHE GLU LYS GLN LEU SEQRES 6 D 276 GLU THR ALA LEU SER ILE GLY PRO ASP ALA ILE LYS THR SEQRES 7 D 276 GLY MET LEU GLY THR GLU GLU ILE ILE LYS ARG ALA GLY SEQRES 8 D 276 GLU VAL TYR GLU ALA SER ASN ALA GLN TYR PHE VAL VAL SEQRES 9 D 276 ASP PRO VAL MET VAL CYS LYS GLY GLU ASP GLU VAL LEU SEQRES 10 D 276 ASN PRO GLY ASN THR GLU ALA MET ILE LYS TYR LEU LEU SEQRES 11 D 276 PRO LYS ALA THR VAL VAL THR PRO ASN LEU PHE GLU ALA SEQRES 12 D 276 GLY GLN LEU SER GLY LEU GLY LYS LEU ASN SER ILE GLU SEQRES 13 D 276 ASP MET LYS LYS ALA ALA THR ILE ILE PHE ASP LYS GLY SEQRES 14 D 276 ALA GLN HIS VAL ILE ILE LYS GLY GLY LYS ALA LEU ASP SEQRES 15 D 276 GLN ASP LYS SER TYR ASP LEU TYR TYR ASP GLY GLN THR SEQRES 16 D 276 PHE TYR GLN LEU THR THR ASP MET PHE GLN GLN SER TYR SEQRES 17 D 276 ASN HIS GLY ALA GLY CYS THR PHE ALA ALA ALA THR THR SEQRES 18 D 276 ALA TYR LEU ALA ASN GLY LYS SER PRO LYS GLU ALA VAL SEQRES 19 D 276 ILE SER ALA LYS ALA PHE VAL ALA SER ALA ILE LYS ASN SEQRES 20 D 276 GLY TRP LYS MET ASN ASP PHE VAL GLY PRO VAL ASP HIS SEQRES 21 D 276 GLY ALA TYR ASN ARG ILE GLU HIS ILE ASP VAL GLU VAL SEQRES 22 D 276 THR GLU VAL HET PXL A 300 12 HET ACP A 500 62 HET PXL B 300 12 HET ACP B 500 31 HET SO4 B1277 5 HET SO4 B1278 5 HET PXL C 300 12 HET ACP C 500 31 HET SO4 C1277 5 HET SO4 C1278 5 HET UEG D 300 12 HET ACP D 500 31 HET SO4 D1277 5 HET SO4 D1278 5 HET SO4 D1279 5 HETNAM PXL 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE HETNAM ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER HETNAM SO4 SULFATE ION HETNAM UEG 4,5-BIS(HYDROXYMETHYL)-2-METHYL-PYRIDIN-3-OL HETSYN PXL PYRIDOXAL HETSYN ACP ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE FORMUL 5 PXL 3(C8 H9 N O3) FORMUL 6 ACP 4(C11 H18 N5 O12 P3) FORMUL 9 SO4 7(O4 S 2-) FORMUL 15 UEG C8 H11 N O3 FORMUL 20 HOH *313(H2 O) HELIX 1 1 ALA A 18 LEU A 30 1 13 HELIX 2 2 PRO A 57 GLY A 72 1 16 HELIX 3 3 THR A 83 SER A 97 1 15 HELIX 4 4 ASN A 118 LEU A 129 1 12 HELIX 5 5 LEU A 130 ALA A 133 5 4 HELIX 6 6 ASN A 139 GLY A 148 1 10 HELIX 7 7 SER A 154 LYS A 168 1 15 HELIX 8 8 GLY A 178 LEU A 181 5 4 HELIX 9 9 GLY A 211 ASN A 226 1 16 HELIX 10 10 SER A 229 ASN A 247 1 19 HELIX 11 11 GLY A 261 ILE A 266 1 6 HELIX 12 12 ALA B 18 LEU B 30 1 13 HELIX 13 13 PRO B 57 GLY B 72 1 16 HELIX 14 14 THR B 83 SER B 97 1 15 HELIX 15 15 ASN B 118 LEU B 129 1 12 HELIX 16 16 LEU B 130 ALA B 133 5 4 HELIX 17 17 ASN B 139 SER B 147 1 9 HELIX 18 18 SER B 154 LYS B 168 1 15 HELIX 19 19 GLY B 178 LEU B 181 5 4 HELIX 20 20 GLY B 211 ASN B 226 1 16 HELIX 21 21 SER B 229 ASN B 247 1 19 HELIX 22 22 GLY B 261 ILE B 266 1 6 HELIX 23 23 ALA C 18 LEU C 30 1 13 HELIX 24 24 PRO C 57 GLY C 72 1 16 HELIX 25 25 THR C 83 SER C 97 1 15 HELIX 26 26 ASN C 118 LEU C 129 1 12 HELIX 27 27 LEU C 130 ALA C 133 5 4 HELIX 28 28 ASN C 139 GLY C 148 1 10 HELIX 29 29 SER C 154 LYS C 168 1 15 HELIX 30 30 GLY C 177 ASP C 182 1 6 HELIX 31 31 GLY C 211 ASN C 226 1 16 HELIX 32 32 SER C 229 ASN C 247 1 19 HELIX 33 33 GLY C 261 ILE C 266 1 6 HELIX 34 34 ALA D 18 LEU D 30 1 13 HELIX 35 35 PRO D 57 GLY D 72 1 16 HELIX 36 36 THR D 83 SER D 97 1 15 HELIX 37 37 PRO D 119 LEU D 129 1 11 HELIX 38 38 LEU D 130 ALA D 133 5 4 HELIX 39 39 ASN D 139 GLY D 148 1 10 HELIX 40 40 SER D 154 LYS D 168 1 15 HELIX 41 41 GLY D 178 ASP D 182 5 5 HELIX 42 42 GLY D 211 ASN D 226 1 16 HELIX 43 43 SER D 229 ASN D 247 1 19 HELIX 44 44 GLY D 261 ILE D 266 1 6 SHEET 1 AA 6 HIS A 51 PRO A 55 0 SHEET 2 AA 6 TYR A 33 MET A 44 -1 O ILE A 41 N THR A 54 SHEET 3 AA 6 LYS A 5 ASP A 13 1 O VAL A 6 N MET A 35 SHEET 4 AA 6 ALA A 75 THR A 78 1 O ALA A 75 N LEU A 7 SHEET 5 AA 6 TYR A 101 VAL A 104 1 O TYR A 101 N ILE A 76 SHEET 6 AA 6 VAL A 135 VAL A 136 1 O VAL A 135 N VAL A 104 SHEET 1 AB 4 VAL A 173 LYS A 176 0 SHEET 2 AB 4 LYS A 185 TYR A 191 -1 O LEU A 189 N ILE A 175 SHEET 3 AB 4 PHE A 196 ASP A 202 -1 O TYR A 197 N TYR A 190 SHEET 4 AB 4 GLU A 272 GLU A 275 -1 O GLU A 272 N THR A 200 SHEET 1 BA 6 HIS B 51 PRO B 55 0 SHEET 2 BA 6 TYR B 33 MET B 44 -1 O ILE B 41 N THR B 54 SHEET 3 BA 6 LYS B 5 ASP B 13 1 O VAL B 6 N MET B 35 SHEET 4 BA 6 ALA B 75 THR B 78 1 O ALA B 75 N LEU B 7 SHEET 5 BA 6 TYR B 101 VAL B 104 1 O TYR B 101 N ILE B 76 SHEET 6 BA 6 VAL B 135 VAL B 136 1 O VAL B 135 N VAL B 104 SHEET 1 BB 4 VAL B 173 LYS B 176 0 SHEET 2 BB 4 LYS B 185 TYR B 191 -1 O LEU B 189 N ILE B 175 SHEET 3 BB 4 PHE B 196 ASP B 202 -1 O TYR B 197 N TYR B 190 SHEET 4 BB 4 GLU B 272 GLU B 275 -1 O GLU B 272 N THR B 200 SHEET 1 CA 6 HIS C 51 PRO C 55 0 SHEET 2 CA 6 TYR C 33 MET C 44 -1 O ILE C 41 N THR C 54 SHEET 3 CA 6 LYS C 5 ASP C 13 1 O VAL C 6 N MET C 35 SHEET 4 CA 6 ALA C 75 THR C 78 1 O ALA C 75 N LEU C 7 SHEET 5 CA 6 TYR C 101 VAL C 104 1 O TYR C 101 N ILE C 76 SHEET 6 CA 6 VAL C 135 VAL C 136 1 O VAL C 135 N VAL C 104 SHEET 1 CB 4 VAL C 173 LYS C 176 0 SHEET 2 CB 4 LYS C 185 TYR C 191 -1 O LEU C 189 N ILE C 175 SHEET 3 CB 4 PHE C 196 ASP C 202 -1 O TYR C 197 N TYR C 190 SHEET 4 CB 4 GLU C 272 GLU C 275 -1 O GLU C 272 N THR C 200 SHEET 1 DA 6 HIS D 51 PRO D 55 0 SHEET 2 DA 6 TYR D 33 MET D 44 -1 O ILE D 41 N THR D 54 SHEET 3 DA 6 LYS D 5 ASP D 13 1 O VAL D 6 N MET D 35 SHEET 4 DA 6 ALA D 75 THR D 78 1 O ALA D 75 N LEU D 7 SHEET 5 DA 6 TYR D 101 VAL D 104 1 O TYR D 101 N ILE D 76 SHEET 6 DA 6 VAL D 135 VAL D 136 1 O VAL D 135 N VAL D 104 SHEET 1 DB 4 VAL D 173 LYS D 176 0 SHEET 2 DB 4 LYS D 185 TYR D 191 -1 O LEU D 189 N ILE D 175 SHEET 3 DB 4 PHE D 196 ASP D 202 -1 O TYR D 197 N TYR D 190 SHEET 4 DB 4 GLU D 272 GLU D 275 -1 O GLU D 272 N THR D 200 LINK SG CYS D 110 C4A UEG D 300 1555 1555 1.67 SITE 1 AC1 7 GLY A 11 SER A 12 ASP A 13 GLY A 19 SITE 2 AC1 7 CYS A 214 ACP A 500 HOH A2007 SITE 1 AC2 18 LYS A 176 SER A 186 ASP A 188 ASP A 202 SITE 2 AC2 18 MET A 203 PHE A 204 GLN A 205 ASN A 209 SITE 3 AC2 18 HIS A 210 GLY A 211 ALA A 212 GLY A 213 SITE 4 AC2 18 CYS A 214 LYS A 238 ILE A 245 PXL A 300 SITE 5 AC2 18 HOH A2051 HOH A2056 SITE 1 AC3 11 GLY B 11 SER B 12 ASP B 13 GLY B 19 SITE 2 AC3 11 VAL B 42 MET B 80 VAL B 107 HIS B 210 SITE 3 AC3 11 CYS B 214 ACP B 500 HOH B2005 SITE 1 AC4 22 LYS B 176 GLY B 178 SER B 186 ASP B 188 SITE 2 AC4 22 ASP B 202 MET B 203 PHE B 204 GLN B 205 SITE 3 AC4 22 GLN B 206 ASN B 209 HIS B 210 GLY B 211 SITE 4 AC4 22 ALA B 212 GLY B 213 CYS B 214 LYS B 238 SITE 5 AC4 22 ILE B 245 PXL B 300 HOH B2053 HOH B2054 SITE 6 AC4 22 HOH B2062 HOH B2085 SITE 1 AC5 5 GLY C 11 GLY C 19 CYS C 214 ACP C 500 SITE 2 AC5 5 HOH C2009 SITE 1 AC6 21 LYS C 176 GLY C 178 LYS C 179 SER C 186 SITE 2 AC6 21 ASP C 188 ASP C 202 MET C 203 PHE C 204 SITE 3 AC6 21 GLN C 205 ASN C 209 HIS C 210 GLY C 211 SITE 4 AC6 21 ALA C 212 GLY C 213 CYS C 214 LYS C 238 SITE 5 AC6 21 ILE C 245 PXL C 300 HOH C2047 HOH C2048 SITE 6 AC6 21 HOH C2058 SITE 1 AC7 9 GLY D 11 GLY D 19 VAL D 42 VAL D 109 SITE 2 AC7 9 CYS D 110 HIS D 210 CYS D 214 HOH D2003 SITE 3 AC7 9 HOH D2016 SITE 1 AC8 17 ASN D 139 LYS D 176 GLY D 178 SER D 186 SITE 2 AC8 17 ASP D 188 ASP D 202 PHE D 204 GLN D 205 SITE 3 AC8 17 ASN D 209 GLY D 211 ALA D 212 GLY D 213 SITE 4 AC8 17 CYS D 214 LYS D 238 ILE D 245 HOH D2035 SITE 5 AC8 17 HOH D2036 SITE 1 AC9 5 GLN C 205 GLN C 206 SER C 207 THR D 274 SITE 2 AC9 5 GLU D 275 SITE 1 BC1 2 GLN D 206 SER D 207 SITE 1 BC2 3 GLY D 72 ASN D 98 HOH D2019 SITE 1 BC3 3 LEU D 30 TYR D 223 TYR D 263 SITE 1 BC4 3 GLY B 72 ASN B 98 HOH B2038 SITE 1 BC5 3 LYS A 185 HIS B 172 HOH B2074 SITE 1 BC6 3 GLY C 72 ASN C 98 HOH C2008 CRYST1 62.190 100.660 168.210 90.00 90.00 90.00 P 21 21 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016080 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005945 0.00000 MTRIX1 1 0.998600 0.008800 -0.051500 4.50860 1 MTRIX2 1 -0.011700 0.998300 -0.056700 -1.32770 1 MTRIX3 1 0.050900 0.057200 0.997100 43.35100 1 MTRIX1 2 -0.995200 -0.010800 -0.097700 -35.31840 1 MTRIX2 2 0.006300 -0.998900 0.046400 -0.51330 1 MTRIX3 2 -0.098100 0.045500 0.994100 40.37110 1 MTRIX1 3 -0.986000 -0.007000 -0.166500 -23.64360 1 MTRIX2 3 0.007200 -1.000000 -0.000400 -1.64050 1 MTRIX3 3 -0.166500 -0.001600 0.986000 -1.94640 1