HEADER TRANSFERASE/DNA 27-JUL-14 4QZ9 TITLE MOUSE TDT IN COMPLEX WITH A DSB SUBSTRATE, C-A BASE PAIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA NUCLEOTIDYLEXOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEE REMARK 999; COMPND 5 SYNONYM: TERMINAL ADDITION ENZYME, TERMINAL COMPND 6 DEOXYNUCLEOTIDYLTRANSFERASE, TDT, TERMINAL TRANSFERASE; COMPND 7 EC: 2.7.7.31; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*AP*AP*AP*AP*AP*C)-3'; COMPND 11 CHAIN: D, U; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*TP*TP*TP*TP*TP*GP*A)-3'; COMPND 15 CHAIN: T; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DNTT, TDT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS TERMINAL DEOXYNUCLEOTIDYLTRANSFERASE, NUCLEUS, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.GOUGE,M.DELARUE REVDAT 3 20-SEP-23 4QZ9 1 REMARK SEQADV LINK REVDAT 2 26-JUL-17 4QZ9 1 SOURCE REMARK REVDAT 1 10-JUN-15 4QZ9 0 JRNL AUTH J.GOUGE,S.ROSARIO,F.ROMAIN,F.POITEVIN,P.BEGUIN,M.DELARUE JRNL TITL STRUCTURAL BASIS FOR A NOVEL MECHANISM OF DNA BRIDGING AND JRNL TITL 2 ALIGNMENT IN EUKARYOTIC DSB DNA REPAIR. JRNL REF EMBO J. V. 34 1126 2015 JRNL REFN ISSN 0261-4189 JRNL PMID 25762590 JRNL DOI 10.15252/EMBJ.201489643 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 32367 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 1647 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 16 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.54 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2831 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2154 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2669 REMARK 3 BIN R VALUE (WORKING SET) : 0.2155 REMARK 3 BIN FREE R VALUE : 0.2133 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.72 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 162 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2786 REMARK 3 NUCLEIC ACID ATOMS : 366 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.52770 REMARK 3 B22 (A**2) : 3.29940 REMARK 3 B33 (A**2) : -5.82710 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.44980 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.272 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.175 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.141 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.166 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.138 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3303 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4538 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1429 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 72 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 435 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3303 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 423 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3883 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.97 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.91 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 3.13 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: {A|147 - 237} REMARK 3 ORIGIN FOR THE GROUP (A): 7.9918 -9.3870 19.7464 REMARK 3 T TENSOR REMARK 3 T11: -0.0296 T22: -0.0327 REMARK 3 T33: -0.0730 T12: 0.1500 REMARK 3 T13: 0.0534 T23: 0.0246 REMARK 3 L TENSOR REMARK 3 L11: 1.3982 L22: 4.2046 REMARK 3 L33: 1.2527 L12: -0.8638 REMARK 3 L13: 0.0052 L23: 0.0099 REMARK 3 S TENSOR REMARK 3 S11: 0.0986 S12: 0.0478 S13: -0.0740 REMARK 3 S21: -0.2320 S22: -0.1062 S23: -0.4579 REMARK 3 S31: -0.0047 S32: 0.2101 S33: 0.0076 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: {A|238 - 431} REMARK 3 ORIGIN FOR THE GROUP (A): 2.5656 4.5030 45.2675 REMARK 3 T TENSOR REMARK 3 T11: -0.0669 T22: -0.0287 REMARK 3 T33: -0.0506 T12: 0.0288 REMARK 3 T13: -0.0105 T23: 0.0663 REMARK 3 L TENSOR REMARK 3 L11: 1.8973 L22: 1.3858 REMARK 3 L33: 0.7544 L12: 0.3247 REMARK 3 L13: -0.1460 L23: 0.2107 REMARK 3 S TENSOR REMARK 3 S11: 0.0800 S12: -0.2155 S13: 0.1051 REMARK 3 S21: 0.0732 S22: -0.1142 S23: -0.2240 REMARK 3 S31: -0.0323 S32: 0.0371 S33: 0.0342 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: {A|432 - 510} REMARK 3 ORIGIN FOR THE GROUP (A): -13.3881 0.0302 27.8330 REMARK 3 T TENSOR REMARK 3 T11: 0.0013 T22: -0.0587 REMARK 3 T33: -0.0371 T12: 0.0885 REMARK 3 T13: 0.0014 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.2953 L22: 0.9410 REMARK 3 L33: 1.9933 L12: -0.2978 REMARK 3 L13: 0.2563 L23: -0.2135 REMARK 3 S TENSOR REMARK 3 S11: 0.0835 S12: 0.0534 S13: -0.0320 REMARK 3 S21: -0.1220 S22: -0.1381 S23: 0.2186 REMARK 3 S31: -0.0032 S32: -0.0920 S33: 0.0546 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: {T|1 - 7} REMARK 3 ORIGIN FOR THE GROUP (A): -0.8207 8.0666 14.0644 REMARK 3 T TENSOR REMARK 3 T11: 0.1602 T22: -0.0215 REMARK 3 T33: -0.1443 T12: 0.1038 REMARK 3 T13: 0.0532 T23: 0.0694 REMARK 3 L TENSOR REMARK 3 L11: 1.1651 L22: 0.8099 REMARK 3 L33: 1.3337 L12: 1.6636 REMARK 3 L13: -0.4186 L23: 1.5380 REMARK 3 S TENSOR REMARK 3 S11: 0.0124 S12: 0.1331 S13: -0.0027 REMARK 3 S21: -0.3480 S22: 0.1986 S23: 0.2821 REMARK 3 S31: -0.4977 S32: 0.2303 S33: -0.2111 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: {U|1 - 6} REMARK 3 ORIGIN FOR THE GROUP (A): 4.2851 16.2558 36.1796 REMARK 3 T TENSOR REMARK 3 T11: -0.0542 T22: -0.1782 REMARK 3 T33: 0.2487 T12: 0.0292 REMARK 3 T13: 0.0560 T23: 0.1570 REMARK 3 L TENSOR REMARK 3 L11: 2.5905 L22: 0.0000 REMARK 3 L33: 1.3195 L12: -2.2365 REMARK 3 L13: -1.7840 L23: -2.0228 REMARK 3 S TENSOR REMARK 3 S11: -0.0076 S12: -0.0929 S13: 0.1405 REMARK 3 S21: -0.0915 S22: -0.0914 S23: 0.1382 REMARK 3 S31: -0.1269 S32: -0.0983 S33: 0.0990 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: {D|1 - 6} REMARK 3 ORIGIN FOR THE GROUP (A): 1.2572 1.4218 8.5126 REMARK 3 T TENSOR REMARK 3 T11: 0.0392 T22: 0.0485 REMARK 3 T33: -0.1146 T12: 0.1050 REMARK 3 T13: 0.0040 T23: 0.0278 REMARK 3 L TENSOR REMARK 3 L11: 0.6435 L22: 4.4578 REMARK 3 L33: 5.3909 L12: 0.9483 REMARK 3 L13: -2.2908 L23: -2.4258 REMARK 3 S TENSOR REMARK 3 S11: 0.0279 S12: 0.0597 S13: -0.1911 REMARK 3 S21: -0.2198 S22: 0.0746 S23: 0.1566 REMARK 3 S31: -0.0091 S32: -0.2992 S33: -0.1024 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.919600 REMARK 200 MONOCHROMATOR : CHANNEL CUT CRYOGENICALLY COOLED REMARK 200 CRYSTAL REMARK 200 OPTICS : KIRKPATRICK-BAEZ PAIR OF BI REMARK 200 -MORPH MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32370 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 4I2A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12-17% PEG4000, 9-12% ISOPROPANOL, 100 REMARK 280 MM SODIUM ACETATE, 100 MM HEPES, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.46800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.46800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.36000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, T, U 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 MET A 111 REMARK 465 GLY A 112 REMARK 465 SER A 113 REMARK 465 SER A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 SER A 121 REMARK 465 SER A 122 REMARK 465 GLY A 123 REMARK 465 LEU A 124 REMARK 465 VAL A 125 REMARK 465 PRO A 126 REMARK 465 ARG A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 HIS A 130 REMARK 465 MET A 131 REMARK 465 SER A 132 REMARK 465 PRO A 133 REMARK 465 SER A 134 REMARK 465 PRO A 135 REMARK 465 VAL A 136 REMARK 465 PRO A 137 REMARK 465 GLY A 138 REMARK 465 SER A 139 REMARK 465 GLN A 140 REMARK 465 ASN A 141 REMARK 465 VAL A 142 REMARK 465 PRO A 143 REMARK 465 ALA A 144 REMARK 465 PRO A 145 REMARK 465 ALA A 146 REMARK 465 GLN A 390 REMARK 465 PRO A 391 REMARK 465 SER A 392 REMARK 465 ARG A 393 REMARK 465 LYS A 394 REMARK 465 VAL A 395 REMARK 465 ASP A 396 REMARK 465 GLU A 418 REMARK 465 LYS A 419 REMARK 465 SER A 420 REMARK 465 GLY A 421 REMARK 465 GLN A 422 REMARK 465 GLN A 423 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 VAL A 147 CG1 CG2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 GLU A 185 CG CD OE1 OE2 REMARK 470 LYS A 209 CG CD CE NZ REMARK 470 GLU A 212 CG CD OE1 OE2 REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 LYS A 238 CG CD CE NZ REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 GLU A 317 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLU A 386 CG CD OE1 OE2 REMARK 470 LYS A 387 CG CD CE NZ REMARK 470 PHE A 388 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 389 CG CD CE NZ REMARK 470 DC D 6 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DC D 6 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC D 6 C6 REMARK 470 DC U 6 O3' 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 DT T 1 O4' - C1' - N1 ANGL. DEV. = 2.0 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 CYS A 302 154.24 64.97 REMARK 500 THR A 331 -153.76 -114.69 REMARK 500 ASN A 509 45.68 -84.46 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 NA A 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 253 O REMARK 620 2 VAL A 255 O 89.7 REMARK 620 3 VAL A 258 O 100.1 99.8 REMARK 620 4 HOH A 847 O 79.9 85.7 174.5 REMARK 620 5 DA U 5 OP1 162.9 100.2 92.1 86.8 REMARK 620 6 HOH U 102 O 89.5 178.8 81.1 93.4 80.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD1 REMARK 620 2 ASP A 345 OD2 91.2 REMARK 620 3 DCT A 604 O2B 171.8 96.4 REMARK 620 4 DCT A 604 O2G 88.0 176.2 84.2 REMARK 620 5 DCT A 604 O2A 91.6 89.2 91.5 94.6 REMARK 620 6 HOH A 849 O 88.8 90.1 88.2 86.2 179.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 343 OD2 REMARK 620 2 ASP A 345 OD1 75.0 REMARK 620 3 ASP A 434 OD2 79.8 78.0 REMARK 620 4 DCT A 604 O2A 78.8 85.7 155.8 REMARK 620 N 1 2 3 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCT A 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4I27 RELATED DB: PDB REMARK 900 RELATED ID: 1JMS RELATED DB: PDB REMARK 900 RELATED ID: 4QZ8 RELATED DB: PDB REMARK 900 RELATED ID: 4QZA RELATED DB: PDB REMARK 900 RELATED ID: 4QZB RELATED DB: PDB REMARK 900 RELATED ID: 4QZC RELATED DB: PDB REMARK 900 RELATED ID: 4QZD RELATED DB: PDB REMARK 900 RELATED ID: 4QZE RELATED DB: PDB REMARK 900 RELATED ID: 4QZF RELATED DB: PDB REMARK 900 RELATED ID: 4QZG RELATED DB: PDB REMARK 900 RELATED ID: 4QZH RELATED DB: PDB REMARK 900 RELATED ID: 4QZI RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 PROTEIN COMPRISES UNP RESIDUES 132-482 AND 503-530 WITH 483-502 REMARK 999 DELETED. DBREF 4QZ9 A 132 482 UNP P09838 TDT_MOUSE 132 482 DBREF 4QZ9 A 483 510 UNP P09838 TDT_MOUSE 503 530 DBREF 4QZ9 D 1 6 PDB 4QZ9 4QZ9 1 6 DBREF 4QZ9 U 1 6 PDB 4QZ9 4QZ9 1 6 DBREF 4QZ9 T 1 7 PDB 4QZ9 4QZ9 1 7 SEQADV 4QZ9 MET A 111 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 GLY A 112 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 SER A 113 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 SER A 114 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 HIS A 115 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 HIS A 116 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 HIS A 117 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 HIS A 118 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 HIS A 119 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 HIS A 120 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 SER A 121 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 SER A 122 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 GLY A 123 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 LEU A 124 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 VAL A 125 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 PRO A 126 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 ARG A 127 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 GLY A 128 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 SER A 129 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 HIS A 130 UNP P09838 EXPRESSION TAG SEQADV 4QZ9 MET A 131 UNP P09838 EXPRESSION TAG SEQRES 1 A 400 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 400 LEU VAL PRO ARG GLY SER HIS MET SER PRO SER PRO VAL SEQRES 3 A 400 PRO GLY SER GLN ASN VAL PRO ALA PRO ALA VAL LYS LYS SEQRES 4 A 400 ILE SER GLN TYR ALA CYS GLN ARG ARG THR THR LEU ASN SEQRES 5 A 400 ASN TYR ASN GLN LEU PHE THR ASP ALA LEU ASP ILE LEU SEQRES 6 A 400 ALA GLU ASN ASP GLU LEU ARG GLU ASN GLU GLY SER CYS SEQRES 7 A 400 LEU ALA PHE MET ARG ALA SER SER VAL LEU LYS SER LEU SEQRES 8 A 400 PRO PHE PRO ILE THR SER MET LYS ASP THR GLU GLY ILE SEQRES 9 A 400 PRO CYS LEU GLY ASP LYS VAL LYS SER ILE ILE GLU GLY SEQRES 10 A 400 ILE ILE GLU ASP GLY GLU SER SER GLU ALA LYS ALA VAL SEQRES 11 A 400 LEU ASN ASP GLU ARG TYR LYS SER PHE LYS LEU PHE THR SEQRES 12 A 400 SER VAL PHE GLY VAL GLY LEU LYS THR ALA GLU LYS TRP SEQRES 13 A 400 PHE ARG MET GLY PHE ARG THR LEU SER LYS ILE GLN SER SEQRES 14 A 400 ASP LYS SER LEU ARG PHE THR GLN MET GLN LYS ALA GLY SEQRES 15 A 400 PHE LEU TYR TYR GLU ASP LEU VAL SER CYS VAL ASN ARG SEQRES 16 A 400 PRO GLU ALA GLU ALA VAL SER MET LEU VAL LYS GLU ALA SEQRES 17 A 400 VAL VAL THR PHE LEU PRO ASP ALA LEU VAL THR MET THR SEQRES 18 A 400 GLY GLY PHE ARG ARG GLY LYS MET THR GLY HIS ASP VAL SEQRES 19 A 400 ASP PHE LEU ILE THR SER PRO GLU ALA THR GLU ASP GLU SEQRES 20 A 400 GLU GLN GLN LEU LEU HIS LYS VAL THR ASP PHE TRP LYS SEQRES 21 A 400 GLN GLN GLY LEU LEU LEU TYR CYS ASP ILE LEU GLU SER SEQRES 22 A 400 THR PHE GLU LYS PHE LYS GLN PRO SER ARG LYS VAL ASP SEQRES 23 A 400 ALA LEU ASP HIS PHE GLN LYS CYS PHE LEU ILE LEU LYS SEQRES 24 A 400 LEU ASP HIS GLY ARG VAL HIS SER GLU LYS SER GLY GLN SEQRES 25 A 400 GLN GLU GLY LYS GLY TRP LYS ALA ILE ARG VAL ASP LEU SEQRES 26 A 400 VAL MET CYS PRO TYR ASP ARG ARG ALA PHE ALA LEU LEU SEQRES 27 A 400 GLY TRP THR GLY SER ARG GLN PHE GLU ARG ASP LEU ARG SEQRES 28 A 400 ARG TYR ALA THR HIS GLU ARG LYS MET MET LEU ASP ASN SEQRES 29 A 400 HIS ALA LEU TYR ASP ARG THR LYS ARG VAL PHE LEU GLU SEQRES 30 A 400 ALA GLU SER GLU GLU GLU ILE PHE ALA HIS LEU GLY LEU SEQRES 31 A 400 ASP TYR ILE GLU PRO TRP GLU ARG ASN ALA SEQRES 1 D 6 DA DA DA DA DA DC SEQRES 1 T 7 DT DT DT DT DT DG DA SEQRES 1 U 6 DA DA DA DA DA DC HET MG A 601 1 HET MG A 602 1 HET NA A 603 1 HET DCT A 604 27 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE FORMUL 5 MG 2(MG 2+) FORMUL 7 NA NA 1+ FORMUL 8 DCT C9 H16 N3 O12 P3 FORMUL 9 HOH *337(H2 O) HELIX 1 1 TYR A 153 ARG A 157 5 5 HELIX 2 2 ASN A 165 ARG A 182 1 18 HELIX 3 3 ASN A 184 SER A 200 1 17 HELIX 4 4 SER A 207 GLU A 212 5 6 HELIX 5 5 GLY A 218 GLY A 232 1 15 HELIX 6 6 SER A 234 ASP A 243 1 10 HELIX 7 7 ASP A 243 SER A 254 1 12 HELIX 8 8 GLY A 259 MET A 269 1 11 HELIX 9 9 THR A 273 ASP A 280 1 8 HELIX 10 10 THR A 286 TYR A 295 1 10 HELIX 11 11 TYR A 295 SER A 301 1 7 HELIX 12 12 ARG A 305 LEU A 323 1 19 HELIX 13 13 THR A 331 ARG A 336 1 6 HELIX 14 14 THR A 354 GLN A 372 1 19 HELIX 15 15 GLY A 413 VAL A 415 5 3 HELIX 16 16 PRO A 439 ASP A 441 5 3 HELIX 17 17 ARG A 442 GLY A 452 1 11 HELIX 18 18 SER A 453 LYS A 469 1 17 HELIX 19 19 SER A 490 LEU A 498 1 9 HELIX 20 20 GLU A 504 ARG A 508 5 5 SHEET 1 A 2 VAL A 303 ASN A 304 0 SHEET 2 A 2 THR A 340 GLY A 341 -1 O GLY A 341 N VAL A 303 SHEET 1 B 5 LEU A 327 MET A 330 0 SHEET 2 B 5 VAL A 344 THR A 349 -1 O THR A 349 N LEU A 327 SHEET 3 B 5 TRP A 428 MET A 437 1 O VAL A 436 N ILE A 348 SHEET 4 B 5 GLN A 402 ASP A 411 -1 N LEU A 406 O VAL A 433 SHEET 5 B 5 LEU A 375 LEU A 381 -1 N LEU A 381 O LYS A 403 SHEET 1 C 3 MET A 470 LEU A 472 0 SHEET 2 C 3 LEU A 477 ASP A 479 -1 O TYR A 478 N MET A 471 SHEET 3 C 3 VAL A 484 LEU A 486 -1 O LEU A 486 N LEU A 477 LINK O THR A 253 NA NA A 603 1555 1555 2.43 LINK O VAL A 255 NA NA A 603 1555 1555 2.42 LINK O VAL A 258 NA NA A 603 1555 1555 2.28 LINK OD1 ASP A 343 MG MG A 601 1555 1555 2.01 LINK OD2 ASP A 343 MG MG A 602 1555 1555 2.24 LINK OD2 ASP A 345 MG MG A 601 1555 1555 2.24 LINK OD1 ASP A 345 MG MG A 602 1555 1555 2.49 LINK OD2 ASP A 434 MG MG A 602 1555 1555 2.24 LINK MG MG A 601 O2B DCT A 604 1555 1555 2.08 LINK MG MG A 601 O2G DCT A 604 1555 1555 2.11 LINK MG MG A 601 O2A DCT A 604 1555 1555 2.11 LINK MG MG A 601 O HOH A 849 1555 1555 2.21 LINK MG MG A 602 O2A DCT A 604 1555 1555 2.78 LINK NA NA A 603 O HOH A 847 1555 1555 2.42 LINK NA NA A 603 OP1 DA U 5 1555 1555 2.63 LINK NA NA A 603 O HOH U 102 1555 1555 2.66 CISPEP 1 GLY A 452 SER A 453 0 -1.27 SITE 1 AC1 4 ASP A 343 ASP A 345 DCT A 604 HOH A 849 SITE 1 AC2 5 ASP A 343 ASP A 345 ASP A 434 DCT A 604 SITE 2 AC2 5 DC U 6 SITE 1 AC3 6 THR A 253 VAL A 255 VAL A 258 HOH A 847 SITE 2 AC3 6 DA U 5 HOH U 102 SITE 1 AC4 22 GLY A 332 GLY A 333 ARG A 336 LYS A 338 SITE 2 AC4 22 GLY A 341 HIS A 342 ASP A 343 ASP A 345 SITE 3 AC4 22 GLY A 449 TRP A 450 GLY A 452 ARG A 454 SITE 4 AC4 22 GLU A 457 MG A 601 MG A 602 HOH A 709 SITE 5 AC4 22 HOH A 836 HOH A 849 HOH A 879 HOH A 963 SITE 6 AC4 22 DG T 6 DC U 6 CRYST1 56.936 74.720 126.357 90.00 100.06 90.00 C 1 2 1 8 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 0.017564 0.000000 0.003116 0.00000 SCALE2 0.000000 0.013383 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008038 0.00000