HEADER TRANSFERASE 09-JUN-17 5O7T TITLE CRYSTAL STRUCTURE OF KLENTAQ MUTANT M747K IN A CLOSED TERNARY COMPLEX TITLE 2 WITH A DG:DCTP BASE PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I, THERMOSTABLE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAQ POLYMERASE 1; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA PRIMER; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA TEMPLATE; COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS AQUATICUS; SOURCE 3 ORGANISM_TAXID: 271; SOURCE 4 GENE: POLA, POL1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BETZ,K.DIEDERICHS,A.MARX REVDAT 3 17-JAN-24 5O7T 1 REMARK LINK REVDAT 2 06-DEC-17 5O7T 1 JRNL REVDAT 1 29-NOV-17 5O7T 0 JRNL AUTH K.BETZ,A.NILFOROUSHAN,L.A.WYSS,K.DIEDERICHS,S.J.STURLA, JRNL AUTH 2 A.MARX JRNL TITL STRUCTURAL BASIS FOR THE SELECTIVE INCORPORATION OF AN JRNL TITL 2 ARTIFICIAL NUCLEOTIDE OPPOSITE A DNA ADDUCT BY A DNA JRNL TITL 3 POLYMERASE. JRNL REF CHEM. COMMUN. (CAMB.) V. 53 12704 2017 JRNL REFN ESSN 1364-548X JRNL PMID 29136072 JRNL DOI 10.1039/C7CC07173F REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2747: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.260 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 112015 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 5694 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.4210 - 5.5822 1.00 3606 203 0.1315 0.1674 REMARK 3 2 5.5822 - 4.4318 1.00 3597 183 0.1128 0.1769 REMARK 3 3 4.4318 - 3.8719 0.99 3576 214 0.1204 0.1871 REMARK 3 4 3.8719 - 3.5180 0.99 3547 224 0.1494 0.2254 REMARK 3 5 3.5180 - 3.2659 0.99 3589 189 0.1613 0.2103 REMARK 3 6 3.2659 - 3.0734 0.99 3588 194 0.1854 0.2559 REMARK 3 7 3.0734 - 2.9195 0.99 3562 197 0.1941 0.2647 REMARK 3 8 2.9195 - 2.7924 0.99 3580 206 0.2104 0.2898 REMARK 3 9 2.7924 - 2.6849 0.99 3541 187 0.1969 0.2337 REMARK 3 10 2.6849 - 2.5923 0.99 3569 204 0.1984 0.2860 REMARK 3 11 2.5923 - 2.5113 0.99 3581 208 0.1871 0.2571 REMARK 3 12 2.5113 - 2.4395 0.99 3561 185 0.1857 0.2557 REMARK 3 13 2.4395 - 2.3753 0.98 3585 145 0.1998 0.2557 REMARK 3 14 2.3753 - 2.3173 0.99 3589 175 0.2164 0.2387 REMARK 3 15 2.3173 - 2.2646 0.99 3506 208 0.2125 0.2652 REMARK 3 16 2.2646 - 2.2164 0.99 3604 143 0.2276 0.3225 REMARK 3 17 2.2164 - 2.1721 0.99 3587 191 0.2419 0.3223 REMARK 3 18 2.1721 - 2.1311 0.98 3528 155 0.2400 0.3257 REMARK 3 19 2.1311 - 2.0930 0.98 3580 187 0.2636 0.2849 REMARK 3 20 2.0930 - 2.0576 0.98 3562 181 0.2782 0.2865 REMARK 3 21 2.0576 - 2.0244 0.98 3498 189 0.2811 0.3202 REMARK 3 22 2.0244 - 1.9932 0.98 3517 204 0.2838 0.3200 REMARK 3 23 1.9932 - 1.9639 0.98 3570 201 0.3024 0.3352 REMARK 3 24 1.9639 - 1.9363 0.98 3492 185 0.3177 0.3536 REMARK 3 25 1.9363 - 1.9101 0.98 3543 199 0.3222 0.3639 REMARK 3 26 1.9101 - 1.8853 0.97 3513 167 0.3296 0.3874 REMARK 3 27 1.8853 - 1.8617 0.98 3506 188 0.3399 0.3507 REMARK 3 28 1.8617 - 1.8393 0.98 3538 227 0.3629 0.3738 REMARK 3 29 1.8393 - 1.8179 0.97 3489 196 0.3720 0.3897 REMARK 3 30 1.8179 - 1.7975 0.90 3217 159 0.3903 0.4032 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 5063 REMARK 3 ANGLE : 1.241 6976 REMARK 3 CHIRALITY : 0.066 765 REMARK 3 PLANARITY : 0.009 832 REMARK 3 DIHEDRAL : 16.324 2992 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 293 THROUGH 433 ) REMARK 3 ORIGIN FOR THE GROUP (A): 39.8719 -42.9763 -18.0055 REMARK 3 T TENSOR REMARK 3 T11: 0.2910 T22: 0.3049 REMARK 3 T33: 0.5852 T12: -0.1009 REMARK 3 T13: 0.1005 T23: -0.0620 REMARK 3 L TENSOR REMARK 3 L11: 0.4733 L22: 0.4583 REMARK 3 L33: 0.6291 L12: -0.3120 REMARK 3 L13: -0.0388 L23: 0.2669 REMARK 3 S TENSOR REMARK 3 S11: -0.0774 S12: 0.0677 S13: -0.4526 REMARK 3 S21: -0.1297 S22: 0.0803 S23: -0.2416 REMARK 3 S31: 0.1149 S32: -0.0092 S33: -0.0077 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 434 THROUGH 562 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.7829 -10.9975 2.4878 REMARK 3 T TENSOR REMARK 3 T11: 0.4913 T22: 0.2446 REMARK 3 T33: 0.3220 T12: -0.0139 REMARK 3 T13: 0.0594 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.9561 L22: 0.5734 REMARK 3 L33: 0.5483 L12: 0.7813 REMARK 3 L13: -0.2984 L23: -0.3528 REMARK 3 S TENSOR REMARK 3 S11: 0.1298 S12: -0.0266 S13: 0.1131 REMARK 3 S21: 0.0212 S22: -0.1020 S23: 0.0470 REMARK 3 S31: -0.5553 S32: 0.0040 S33: -0.0011 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 563 THROUGH 832 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1101 -20.1885 -11.6504 REMARK 3 T TENSOR REMARK 3 T11: 0.3191 T22: 0.4661 REMARK 3 T33: 0.2713 T12: 0.0528 REMARK 3 T13: 0.0133 T23: 0.0565 REMARK 3 L TENSOR REMARK 3 L11: 0.7384 L22: 0.5608 REMARK 3 L33: 1.0412 L12: 0.2452 REMARK 3 L13: -0.0311 L23: 0.0426 REMARK 3 S TENSOR REMARK 3 S11: -0.0383 S12: 0.0866 S13: -0.0430 REMARK 3 S21: -0.1231 S22: 0.0495 S23: 0.0137 REMARK 3 S31: -0.2394 S32: -0.3977 S33: 0.0005 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1174 -23.6408 5.1568 REMARK 3 T TENSOR REMARK 3 T11: 0.2860 T22: 0.3447 REMARK 3 T33: 0.3820 T12: 0.0357 REMARK 3 T13: 0.0100 T23: 0.0683 REMARK 3 L TENSOR REMARK 3 L11: 0.0309 L22: 0.1875 REMARK 3 L33: 0.1151 L12: 0.1573 REMARK 3 L13: -0.0285 L23: -0.0807 REMARK 3 S TENSOR REMARK 3 S11: 0.0271 S12: 0.1889 S13: -0.0018 REMARK 3 S21: 0.2331 S22: -0.2056 S23: -0.1412 REMARK 3 S31: -0.3701 S32: 0.1294 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 201 THROUGH 205 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7724 -21.1789 7.2707 REMARK 3 T TENSOR REMARK 3 T11: 0.4115 T22: 0.5465 REMARK 3 T33: 0.2355 T12: 0.0556 REMARK 3 T13: -0.0622 T23: 0.0729 REMARK 3 L TENSOR REMARK 3 L11: 0.3271 L22: 0.3807 REMARK 3 L33: 0.0499 L12: 0.1246 REMARK 3 L13: -0.1258 L23: -0.0350 REMARK 3 S TENSOR REMARK 3 S11: -0.2027 S12: -0.1266 S13: 0.0200 REMARK 3 S21: 0.5541 S22: -0.1923 S23: -0.4532 REMARK 3 S31: -0.1854 S32: -0.0363 S33: -0.0226 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 206 THROUGH 215 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.4531 -23.2014 5.0931 REMARK 3 T TENSOR REMARK 3 T11: 0.2787 T22: 0.3378 REMARK 3 T33: 0.3501 T12: 0.0330 REMARK 3 T13: 0.0005 T23: 0.0461 REMARK 3 L TENSOR REMARK 3 L11: 0.0441 L22: 0.2665 REMARK 3 L33: 0.2567 L12: 0.0741 REMARK 3 L13: -0.1000 L23: 0.2074 REMARK 3 S TENSOR REMARK 3 S11: -0.0937 S12: 0.0840 S13: -0.5642 REMARK 3 S21: 0.1180 S22: 0.3872 S23: -0.2028 REMARK 3 S31: -0.0792 S32: 0.1328 S33: 0.0049 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 216 THROUGH 216 ) REMARK 3 ORIGIN FOR THE GROUP (A): 50.8867 -33.8401 13.4393 REMARK 3 T TENSOR REMARK 3 T11: 0.3419 T22: 0.4341 REMARK 3 T33: 0.8893 T12: 0.1851 REMARK 3 T13: 0.0556 T23: 0.3800 REMARK 3 L TENSOR REMARK 3 L11: 0.0880 L22: 0.5146 REMARK 3 L33: 0.3800 L12: 0.2134 REMARK 3 L13: -0.1853 L23: -0.4427 REMARK 3 S TENSOR REMARK 3 S11: -0.1546 S12: -0.0176 S13: -0.0228 REMARK 3 S21: 0.1500 S22: 0.0046 S23: 0.0576 REMARK 3 S31: 0.0798 S32: 0.0668 S33: -0.0576 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5O7T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005232. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-16 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 : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 112020 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 47.405 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3M8S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0 .1M MAGNESIUMACETATE, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.46333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 60.92667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 60.92667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.46333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1171 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1180 LIES ON A SPECIAL POSITION. 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 OE2 GLU A 473 HH21 ARG A 476 1.43 REMARK 500 HE ARG A 695 O HOH A 1003 1.45 REMARK 500 HH22 ARG A 704 O HOH A 1004 1.55 REMARK 500 HG SER A 644 O VAL A 649 1.56 REMARK 500 HZ3 LYS A 804 OE2 GLU A 808 1.59 REMARK 500 OP2 DG C 211 O HOH C 301 2.10 REMARK 500 O HOH C 337 O HOH C 339 2.15 REMARK 500 OP2 DT C 212 O HOH C 302 2.16 REMARK 500 OD1 ASP A 578 O HOH A 1001 2.16 REMARK 500 O3 GOL B 202 O HOH B 301 2.17 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 DA B 102 O3' DA B 102 C3' -0.048 REMARK 500 DC B 103 O3' DC B 103 C3' -0.062 REMARK 500 DT C 212 O3' DT C 212 C3' -0.039 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 LEU A 760 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 DG B 108 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC B 109 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG B 110 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC C 210 O5' - P - OP1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT C 212 O5' - P - OP2 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG C 214 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT C 215 O5' - P - OP2 ANGL. DEV. = -6.1 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 ARG A 328 143.19 -170.65 REMARK 500 THR A 399 -168.46 -103.23 REMARK 500 VAL A 433 -69.82 -123.70 REMARK 500 ASP A 496 -62.58 -91.55 REMARK 500 ALA A 521 -71.14 -40.54 REMARK 500 LEU A 522 49.23 -93.90 REMARK 500 HIS A 526 144.02 -175.15 REMARK 500 TYR A 545 -55.99 -125.25 REMARK 500 VAL A 586 -19.71 -151.46 REMARK 500 ASP A 732 -5.25 81.86 REMARK 500 HIS A 784 -57.62 67.58 REMARK 500 TYR A 811 93.58 -172.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD1 REMARK 620 2 TYR A 611 O 83.0 REMARK 620 3 ASP A 785 OD2 91.3 90.2 REMARK 620 4 DCP A 903 O1A 100.2 174.4 85.2 REMARK 620 5 DCP A 903 O1B 175.4 92.4 89.0 84.4 REMARK 620 6 DCP A 903 O1G 89.7 88.1 177.9 96.5 89.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 902 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 OD2 REMARK 620 2 ASP A 785 OD1 113.2 REMARK 620 3 DCP A 903 O1A 105.7 86.0 REMARK 620 4 HOH A1039 O 98.4 92.7 154.2 REMARK 620 5 HOH A1141 O 91.4 155.2 83.9 86.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 309 O REMARK 620 2 HOH B 320 O 93.3 REMARK 620 3 HOH B 324 O 91.4 89.6 REMARK 620 4 HOH B 329 O 173.9 91.4 84.9 REMARK 620 5 HOH B 330 O 85.5 172.0 82.6 89.3 REMARK 620 6 HOH C 342 O 64.1 98.7 154.3 118.8 87.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DCP A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 202 DBREF 5O7T A 293 832 UNP P19821 DPO1_THEAQ 293 832 DBREF 5O7T B 101 112 PDB 5O7T 5O7T 101 112 DBREF 5O7T C 201 216 PDB 5O7T 5O7T 201 216 SEQADV 5O7T LYS A 747 UNP P19821 MET 747 ENGINEERED MUTATION SEQRES 1 A 540 ALA LEU GLU GLU ALA PRO TRP PRO PRO PRO GLU GLY ALA SEQRES 2 A 540 PHE VAL GLY PHE VAL LEU SER ARG LYS GLU PRO MET TRP SEQRES 3 A 540 ALA ASP LEU LEU ALA LEU ALA ALA ALA ARG GLY GLY ARG SEQRES 4 A 540 VAL HIS ARG ALA PRO GLU PRO TYR LYS ALA LEU ARG ASP SEQRES 5 A 540 LEU LYS GLU ALA ARG GLY LEU LEU ALA LYS ASP LEU SER SEQRES 6 A 540 VAL LEU ALA LEU ARG GLU GLY LEU GLY LEU PRO PRO GLY SEQRES 7 A 540 ASP ASP PRO MET LEU LEU ALA TYR LEU LEU ASP PRO SER SEQRES 8 A 540 ASN THR THR PRO GLU GLY VAL ALA ARG ARG TYR GLY GLY SEQRES 9 A 540 GLU TRP THR GLU GLU ALA GLY GLU ARG ALA ALA LEU SER SEQRES 10 A 540 GLU ARG LEU PHE ALA ASN LEU TRP GLY ARG LEU GLU GLY SEQRES 11 A 540 GLU GLU ARG LEU LEU TRP LEU TYR ARG GLU VAL GLU ARG SEQRES 12 A 540 PRO LEU SER ALA VAL LEU ALA HIS MET GLU ALA THR GLY SEQRES 13 A 540 VAL ARG LEU ASP VAL ALA TYR LEU ARG ALA LEU SER LEU SEQRES 14 A 540 GLU VAL ALA GLU GLU ILE ALA ARG LEU GLU ALA GLU VAL SEQRES 15 A 540 PHE ARG LEU ALA GLY HIS PRO PHE ASN LEU ASN SER ARG SEQRES 16 A 540 ASP GLN LEU GLU ARG VAL LEU PHE ASP GLU LEU GLY LEU SEQRES 17 A 540 PRO ALA ILE GLY LYS THR GLU LYS THR GLY LYS ARG SER SEQRES 18 A 540 THR SER ALA ALA VAL LEU GLU ALA LEU ARG GLU ALA HIS SEQRES 19 A 540 PRO ILE VAL GLU LYS ILE LEU GLN TYR ARG GLU LEU THR SEQRES 20 A 540 LYS LEU LYS SER THR TYR ILE ASP PRO LEU PRO ASP LEU SEQRES 21 A 540 ILE HIS PRO ARG THR GLY ARG LEU HIS THR ARG PHE ASN SEQRES 22 A 540 GLN THR ALA THR ALA THR GLY ARG LEU SER SER SER ASP SEQRES 23 A 540 PRO ASN LEU GLN ASN ILE PRO VAL ARG THR PRO LEU GLY SEQRES 24 A 540 GLN ARG ILE ARG ARG ALA PHE ILE ALA GLU GLU GLY TRP SEQRES 25 A 540 LEU LEU VAL ALA LEU ASP TYR SER GLN ILE GLU LEU ARG SEQRES 26 A 540 VAL LEU ALA HIS LEU SER GLY ASP GLU ASN LEU ILE ARG SEQRES 27 A 540 VAL PHE GLN GLU GLY ARG ASP ILE HIS THR GLU THR ALA SEQRES 28 A 540 SER TRP MET PHE GLY VAL PRO ARG GLU ALA VAL ASP PRO SEQRES 29 A 540 LEU MET ARG ARG ALA ALA LYS THR ILE ASN PHE GLY VAL SEQRES 30 A 540 LEU TYR GLY MET SER ALA HIS ARG LEU SER GLN GLU LEU SEQRES 31 A 540 ALA ILE PRO TYR GLU GLU ALA GLN ALA PHE ILE GLU ARG SEQRES 32 A 540 TYR PHE GLN SER PHE PRO LYS VAL ARG ALA TRP ILE GLU SEQRES 33 A 540 LYS THR LEU GLU GLU GLY ARG ARG ARG GLY TYR VAL GLU SEQRES 34 A 540 THR LEU PHE GLY ARG ARG ARG TYR VAL PRO ASP LEU GLU SEQRES 35 A 540 ALA ARG VAL LYS SER VAL ARG GLU ALA ALA GLU ARG LYS SEQRES 36 A 540 ALA PHE ASN MET PRO VAL GLN GLY THR ALA ALA ASP LEU SEQRES 37 A 540 MET LYS LEU ALA MET VAL LYS LEU PHE PRO ARG LEU GLU SEQRES 38 A 540 GLU MET GLY ALA ARG MET LEU LEU GLN VAL HIS ASP GLU SEQRES 39 A 540 LEU VAL LEU GLU ALA PRO LYS GLU ARG ALA GLU ALA VAL SEQRES 40 A 540 ALA ARG LEU ALA LYS GLU VAL MET GLU GLY VAL TYR PRO SEQRES 41 A 540 LEU ALA VAL PRO LEU GLU VAL GLU VAL GLY ILE GLY GLU SEQRES 42 A 540 ASP TRP LEU SER ALA LYS GLU SEQRES 1 B 12 DG DA DC DC DA DC DG DG DC DG DC DDG SEQRES 1 C 16 DA DA DA DG DC DG DC DG DC DC DG DT DG SEQRES 2 C 16 DG DT DC HET DDG B 112 33 HET MG A 901 1 HET MG A 902 1 HET DCP A 903 40 HET MG B 201 1 HET GOL B 202 12 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DDG C10 H14 N5 O6 P FORMUL 4 MG 3(MG 2+) FORMUL 6 DCP C9 H16 N3 O13 P3 FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *265(H2 O) HELIX 1 AA1 GLU A 337 LEU A 342 1 6 HELIX 2 AA2 ARG A 343 LEU A 345 5 3 HELIX 3 AA3 LEU A 352 GLU A 363 1 12 HELIX 4 AA4 ASP A 372 ASP A 381 1 10 HELIX 5 AA5 THR A 386 GLY A 395 1 10 HELIX 6 AA6 GLU A 401 LEU A 420 1 20 HELIX 7 AA7 GLU A 423 VAL A 433 1 11 HELIX 8 AA8 VAL A 433 GLY A 448 1 16 HELIX 9 AA9 ASP A 452 GLY A 479 1 28 HELIX 10 AB1 SER A 486 ASP A 496 1 11 HELIX 11 AB2 SER A 515 LEU A 522 1 8 HELIX 12 AB3 HIS A 526 TYR A 545 1 20 HELIX 13 AB4 PRO A 548 ILE A 553 5 6 HELIX 14 AB5 THR A 588 ARG A 596 1 9 HELIX 15 AB6 GLN A 613 GLY A 624 1 12 HELIX 16 AB7 ASP A 625 GLU A 634 1 10 HELIX 17 AB8 ASP A 637 GLY A 648 1 12 HELIX 18 AB9 PRO A 650 VAL A 654 5 5 HELIX 19 AC1 ASP A 655 TYR A 671 1 17 HELIX 20 AC2 SER A 674 ALA A 683 1 10 HELIX 21 AC3 PRO A 685 PHE A 700 1 16 HELIX 22 AC4 PRO A 701 GLY A 718 1 18 HELIX 23 AC5 VAL A 737 MET A 775 1 39 HELIX 24 AC6 ARG A 795 GLY A 809 1 15 HELIX 25 AC7 LEU A 828 GLU A 832 5 5 SHEET 1 AA1 4 GLU A 295 ALA A 297 0 SHEET 2 AA1 4 ARG A 331 ARG A 334 1 O VAL A 332 N ALA A 297 SHEET 3 AA1 4 LEU A 321 ARG A 328 -1 N ALA A 326 O HIS A 333 SHEET 4 AA1 4 PHE A 306 LEU A 311 -1 N GLY A 308 O ALA A 325 SHEET 1 AA2 2 ARG A 450 LEU A 451 0 SHEET 2 AA2 2 PHE A 598 ILE A 599 -1 O ILE A 599 N ARG A 450 SHEET 1 AA3 2 ARG A 563 ASN A 565 0 SHEET 2 AA3 2 SER A 575 SER A 577 -1 O SER A 577 N ARG A 563 SHEET 1 AA4 4 ARG A 778 GLN A 782 0 SHEET 2 AA4 4 GLU A 786 PRO A 792 -1 O GLU A 790 N ARG A 778 SHEET 3 AA4 4 TRP A 604 TYR A 611 -1 N VAL A 607 O LEU A 789 SHEET 4 AA4 4 VAL A 819 GLY A 824 -1 O GLY A 824 N LEU A 606 SHEET 1 AA5 2 TYR A 719 GLU A 721 0 SHEET 2 AA5 2 ARG A 727 TYR A 729 -1 O ARG A 728 N VAL A 720 LINK O3' DC B 111 P DDG B 112 1555 1555 1.55 LINK OD1 ASP A 610 MG MG A 901 1555 1555 2.04 LINK OD2 ASP A 610 MG MG A 902 1555 1555 2.13 LINK O TYR A 611 MG MG A 901 1555 1555 2.11 LINK OD2 ASP A 785 MG MG A 901 1555 1555 2.09 LINK OD1 ASP A 785 MG MG A 902 1555 1555 2.16 LINK MG MG A 901 O1A DCP A 903 1555 1555 2.13 LINK MG MG A 901 O1B DCP A 903 1555 1555 2.10 LINK MG MG A 901 O1G DCP A 903 1555 1555 2.07 LINK MG MG A 902 O1A DCP A 903 1555 1555 2.39 LINK MG MG A 902 O HOH A1039 1555 1555 2.40 LINK MG MG A 902 O HOH A1141 1555 1555 2.47 LINK MG MG B 201 O HOH B 309 1555 1555 2.16 LINK MG MG B 201 O HOH B 320 1555 1555 2.02 LINK MG MG B 201 O HOH B 324 1555 1555 2.02 LINK MG MG B 201 O HOH B 329 1555 1555 1.93 LINK MG MG B 201 O HOH B 330 1555 1555 2.28 LINK MG MG B 201 O HOH C 342 1555 1555 2.49 CISPEP 1 TRP A 299 PRO A 300 0 7.15 CISPEP 2 ASP A 578 PRO A 579 0 -0.21 SITE 1 AC1 5 ASP A 610 TYR A 611 ASP A 785 MG A 902 SITE 2 AC1 5 DCP A 903 SITE 1 AC2 6 ASP A 610 ASP A 785 MG A 901 DCP A 903 SITE 2 AC2 6 HOH A1039 HOH A1141 SITE 1 AC3 22 ARG A 573 ASP A 610 TYR A 611 SER A 612 SITE 2 AC3 22 GLN A 613 ILE A 614 GLU A 615 HIS A 639 SITE 3 AC3 22 ARG A 659 LYS A 663 PHE A 667 ASP A 785 SITE 4 AC3 22 MG A 901 MG A 902 HOH A1036 HOH A1079 SITE 5 AC3 22 HOH A1088 HOH A1141 HOH A1151 DDG B 112 SITE 6 AC3 22 HOH B 307 DG C 204 SITE 1 AC4 6 HOH B 309 HOH B 320 HOH B 324 HOH B 329 SITE 2 AC4 6 HOH B 330 HOH C 342 SITE 1 AC5 7 THR A 664 DC B 111 DDG B 112 HOH B 301 SITE 2 AC5 7 HOH B 305 DG C 204 HOH C 326 CRYST1 109.476 109.476 91.390 90.00 90.00 120.00 P 31 2 1 6 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 0.009134 0.005274 0.000000 0.00000 SCALE2 0.000000 0.010548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010942 0.00000