HEADER TRANSFERASE/DNA 17-AUG-10 3OGU TITLE DNA POLYMERASE BETA MUTANT 5P20 COMPLEXED WITH 6BP OF DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7, 4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*CP*AP*TP*CP*TP*G)-3'; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(P*CP*AP*GP*AP*TP*G)-3'; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21 AI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SYNTHETIC OLIGONUCLEOTIDE KEYWDS DNA POLYMERASE, DNA REPAIR, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MARX,K.DIEDERICHS,K.BERGEN REVDAT 4 06-SEP-23 3OGU 1 REMARK SEQADV LINK REVDAT 3 08-NOV-17 3OGU 1 REMARK REVDAT 2 10-AUG-11 3OGU 1 JRNL VERSN REVDAT 1 24-NOV-10 3OGU 0 JRNL AUTH S.GIESEKING,K.BERGEN,F.DI PASQUALE,K.DIEDERICHS,W.WELTE, JRNL AUTH 2 A.MARX JRNL TITL HUMAN DNA POLYMERASE BETA MUTATIONS ALLOWING EFFICIENT JRNL TITL 2 ABASIC SITE BYPASS. JRNL REF J.BIOL.CHEM. V. 286 4011 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21107011 JRNL DOI 10.1074/JBC.M110.176826 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_357) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 41382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2100 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 47.6856 - 4.5500 1.00 2851 168 0.1950 0.2229 REMARK 3 2 4.5500 - 3.6118 1.00 2741 124 0.1586 0.1719 REMARK 3 3 3.6118 - 3.1554 1.00 2649 154 0.1736 0.2048 REMARK 3 4 3.1554 - 2.8669 1.00 2688 143 0.1998 0.2593 REMARK 3 5 2.8669 - 2.6615 1.00 2637 149 0.2061 0.2546 REMARK 3 6 2.6615 - 2.5046 1.00 2635 137 0.2192 0.2746 REMARK 3 7 2.5046 - 2.3791 1.00 2663 111 0.2167 0.2893 REMARK 3 8 2.3791 - 2.2756 1.00 2642 124 0.2165 0.2484 REMARK 3 9 2.2756 - 2.1880 1.00 2614 147 0.2110 0.2488 REMARK 3 10 2.1880 - 2.1125 1.00 2624 146 0.2047 0.2345 REMARK 3 11 2.1125 - 2.0464 1.00 2609 145 0.2244 0.2449 REMARK 3 12 2.0464 - 1.9879 1.00 2605 140 0.2474 0.3217 REMARK 3 13 1.9879 - 1.9356 1.00 2642 134 0.2683 0.3093 REMARK 3 14 1.9356 - 1.8884 0.98 2511 149 0.2845 0.3197 REMARK 3 15 1.8884 - 1.8454 0.84 2171 129 0.3174 0.3483 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 42.74 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.130 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) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 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 : 0.002 2949 REMARK 3 ANGLE : 0.636 4012 REMARK 3 CHIRALITY : 0.043 437 REMARK 3 PLANARITY : 0.002 474 REMARK 3 DIHEDRAL : 14.630 1158 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 10:92) REMARK 3 ORIGIN FOR THE GROUP (A): 52.1981 52.3499 60.3269 REMARK 3 T TENSOR REMARK 3 T11: 0.2145 T22: 0.2260 REMARK 3 T33: 0.2166 T12: -0.0338 REMARK 3 T13: 0.0092 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.9187 L22: 1.6166 REMARK 3 L33: 0.6198 L12: 0.0078 REMARK 3 L13: 0.6776 L23: 0.2250 REMARK 3 S TENSOR REMARK 3 S11: 0.0333 S12: -0.0262 S13: 0.1339 REMARK 3 S21: 0.0017 S22: -0.0701 S23: 0.1711 REMARK 3 S31: 0.1684 S32: 0.1290 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 93:255) REMARK 3 ORIGIN FOR THE GROUP (A): 69.3880 23.3238 52.9345 REMARK 3 T TENSOR REMARK 3 T11: 0.1367 T22: 0.2301 REMARK 3 T33: 0.0495 T12: -0.0464 REMARK 3 T13: -0.0191 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 1.5286 L22: 0.5278 REMARK 3 L33: 0.7211 L12: -0.1484 REMARK 3 L13: -0.7845 L23: -0.1372 REMARK 3 S TENSOR REMARK 3 S11: 0.0196 S12: -0.0640 S13: -0.1703 REMARK 3 S21: -0.0223 S22: -0.0467 S23: 0.0515 REMARK 3 S31: -0.0508 S32: 0.1026 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 256:335) REMARK 3 ORIGIN FOR THE GROUP (A): 72.8909 41.9334 34.0942 REMARK 3 T TENSOR REMARK 3 T11: 0.2268 T22: 0.2662 REMARK 3 T33: 0.1264 T12: -0.0265 REMARK 3 T13: -0.0676 T23: 0.1298 REMARK 3 L TENSOR REMARK 3 L11: 0.9778 L22: 0.6932 REMARK 3 L33: 1.1969 L12: -0.2942 REMARK 3 L13: -0.1602 L23: -0.5402 REMARK 3 S TENSOR REMARK 3 S11: -0.0186 S12: 0.3709 S13: 0.2098 REMARK 3 S21: 0.1220 S22: -0.1084 S23: 0.0088 REMARK 3 S31: -0.1168 S32: -0.1385 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN P AND RESID 1:6) REMARK 3 ORIGIN FOR THE GROUP (A): 50.0098 26.4149 46.9374 REMARK 3 T TENSOR REMARK 3 T11: 0.2383 T22: 0.2732 REMARK 3 T33: 0.2797 T12: -0.0322 REMARK 3 T13: -0.0513 T23: -0.0191 REMARK 3 L TENSOR REMARK 3 L11: 0.0951 L22: 0.0290 REMARK 3 L33: 0.2415 L12: 0.0153 REMARK 3 L13: -0.1203 L23: 0.0448 REMARK 3 S TENSOR REMARK 3 S11: -0.4284 S12: -0.3274 S13: -0.1553 REMARK 3 S21: -0.3242 S22: 0.0135 S23: 0.0608 REMARK 3 S31: -0.8741 S32: -0.1043 S33: -0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN T AND RESID 2:7) REMARK 3 ORIGIN FOR THE GROUP (A): 54.4878 20.9168 45.6279 REMARK 3 T TENSOR REMARK 3 T11: 0.1628 T22: 0.2770 REMARK 3 T33: 0.2273 T12: -0.0704 REMARK 3 T13: -0.0510 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.2846 L22: 0.0560 REMARK 3 L33: 0.0738 L12: -0.1658 REMARK 3 L13: 0.2614 L23: 0.0836 REMARK 3 S TENSOR REMARK 3 S11: 0.1811 S12: 0.1730 S13: 0.0524 REMARK 3 S21: -0.3694 S22: -0.0788 S23: 0.2997 REMARK 3 S31: 0.1894 S32: 0.1577 S33: 0.0000 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 3OGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000061098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 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) : 1.0000 REMARK 200 MONOCHROMATOR : LN2 COOLED FIXED-EXIT SI(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.845 REMARK 200 RESOLUTION RANGE LOW (A) : 47.677 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 1.07100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.430 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.6.1_357 REMARK 200 STARTING MODEL: 9ICW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 0.1 M SODIUM CHLORIDE, REMARK 280 0.1 M MES, PH 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 87.73700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.39100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 87.73700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.39100 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P 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 A 445 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 595 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 GLY A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 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 DC P 1 P DC P 1 OP3 -0.128 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 ASP A 170 114.67 -165.18 REMARK 500 CYS A 178 -144.68 -104.67 REMARK 500 ASP A 246 9.97 86.55 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 336 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 107.6 REMARK 620 3 ILE A 106 O 89.5 84.2 REMARK 620 4 HOH A 618 O 84.2 94.8 173.0 REMARK 620 5 DG P 6 OP1 158.5 91.9 101.8 85.1 REMARK 620 6 HOH P 20 O 74.5 170.1 86.2 95.0 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 NA A 336 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 337 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA P 337 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9ICX RELATED DB: PDB REMARK 900 DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE REMARK 900 PAIRS OF DNA (NON GAPPED DNA ONLY) REMARK 900 RELATED ID: 9ICW RELATED DB: PDB REMARK 900 DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE REMARK 900 PAIRS OF DNA; NATIVE STRUCTURE DBREF 3OGU A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 3OGU T 1 6 PDB 3OGU 3OGU 1 6 DBREF 3OGU P 1 6 PDB 3OGU 3OGU 1 6 SEQADV 3OGU GLY A 2 UNP P06746 SER 2 ENGINEERED MUTATION SEQADV 3OGU LEU A 99 UNP P06746 PHE 99 ENGINEERED MUTATION SEQADV 3OGU LYS A 232 UNP P06746 GLU 232 ENGINEERED MUTATION SEQADV 3OGU MET A 269 UNP P06746 VAL 269 ENGINEERED MUTATION SEQRES 1 A 335 MET GLY LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN LEU LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY LYS THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY MET LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET ARG ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 T 6 DC DA DT DC DT DG SEQRES 1 P 6 DC DA DG DA DT DG HET NA A 336 1 HET GOL A 337 6 HET NA A 338 1 HET MES A 339 12 HET NA P 337 1 HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 NA 3(NA 1+) FORMUL 5 GOL C3 H8 O3 FORMUL 7 MES C6 H13 N O4 S FORMUL 9 HOH *335(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ASP A 91 1 10 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 ASN A 128 1 8 HELIX 9 9 GLU A 129 LEU A 132 5 4 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 LYS A 148 1 7 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 GLY A 179 GLY A 184 5 6 HELIX 14 14 PRO A 208 VAL A 221 1 14 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 LYS A 289 1 15 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 VAL A 177 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O THR A 101 NA NA A 336 1555 1555 2.77 LINK O VAL A 103 NA NA A 336 1555 1555 2.82 LINK O ILE A 106 NA NA A 336 1555 1555 2.79 LINK NA NA A 336 O HOH A 618 1555 1555 2.91 LINK NA NA A 336 OP1 DG P 6 1555 1555 2.63 LINK NA NA A 336 O HOH P 20 1555 1555 3.02 CISPEP 1 GLY A 274 SER A 275 0 0.43 SITE 1 AC1 6 THR A 101 VAL A 103 ILE A 106 HOH A 618 SITE 2 AC1 6 DG P 6 HOH P 20 SITE 1 AC2 8 PRO A 50 HIS A 51 HIS A 134 ILE A 138 SITE 2 AC2 8 THR A 225 ASP A 226 HOH A 359 HOH A 415 SITE 1 AC3 1 MES A 339 SITE 1 AC4 7 GLU A 154 LYS A 244 LYS A 248 TYR A 250 SITE 2 AC4 7 PRO A 251 NA A 338 HOH A 560 SITE 1 AC5 1 DG P 3 CRYST1 175.474 56.782 47.602 90.00 90.00 90.00 P 21 21 2 4 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 0.005699 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017611 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021008 0.00000