PDB Short entry for 2J6U HEADER TRANSFERASE/DNA 04-OCT-06 2J6U TITLE TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6- TITLE 2 METHYLGUANINE MODIFIED DNA, AND DGTP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POL IV; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*T)-3'; COMPND 9 CHAIN: P; COMPND 10 SYNONYM: 14-MER PRIMER; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*TP*CP*AP*C G32P*GP*AP*AP*TP*CP*CP COMPND 14 *TP*TP*CP*CP*CP*CP*C)-3'; COMPND 15 CHAIN: T; COMPND 16 SYNONYM: 18-MER TEMPLATE; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: 5'TCAC G32 GAATCCTTCCCCC3' SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 STRAIN: P2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B/DPO4-NHIS; SOURCE 10 OTHER_DETAILS: GENE DPO4; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS TRANSFERASE/DNA, TRANSFERASE-DNA COMPLEX, MUTATOR PROTEIN, DNA KEYWDS 2 REPLICATION, O6-METHYLGUANINE, TRANSFERASE, METAL-BINDING, DNA KEYWDS 3 POLYMERASE, TRANSLESION DNA SYNTHESIS, DNA-DIRECTED DNA POLYMERASE, KEYWDS 4 DPO4, MAGNESIUM, DNA REPAIR, DNA DAMAGE, DNA-BINDING, KEYWDS 5 NUCLEOTIDYLTRANSFERASE, SULFOLOBUS SOLFATARICUS EXPDTA X-RAY DIFFRACTION AUTHOR R.L.EOFF,A.IRIMIA,F.P.GUENGERICH,M.EGLI REVDAT 5 13-DEC-23 2J6U 1 REMARK LINK REVDAT 4 21-OCT-15 2J6U 1 COMPND SOURCE REMARK VERSN REVDAT 4 2 1 FORMUL SITE REVDAT 3 24-FEB-09 2J6U 1 VERSN REVDAT 2 16-JAN-07 2J6U 1 JRNL REVDAT 1 22-NOV-06 2J6U 0 JRNL AUTH R.L.EOFF,A.IRIMIA,M.EGLI,F.P.GUENGERICH JRNL TITL SULFOLOBUS SOLFATARICUS DNA POLYMERASE DPO4 IS PARTIALLY JRNL TITL 2 INHIBITED BY "WOBBLE" PAIRING BETWEEN O6- METHYLGUANINE AND JRNL TITL 3 CYTOSINE, BUT ACCURATE BYPASS IS PREFERRED. JRNL REF J.BIOL.CHEM. V. 282 1456 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17105728 JRNL DOI 10.1074/JBC.M609661200 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 53192.590 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 17652 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 SET) : 0.217 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 846 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2586 REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE : 0.4190 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 145 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2774 REMARK 3 NUCLEIC ACID ATOMS : 629 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.43000 REMARK 3 B22 (A**2) : 5.40000 REMARK 3 B33 (A**2) : -6.82000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.34 REMARK 3 LOW RESOLUTION CUTOFF (A) : 29.4 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.460 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.720 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.740 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.470 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 41.01 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP1.PARAM REMARK 3 PARAMETER FILE 3 : DGTP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA1.TOP REMARK 3 TOPOLOGY FILE 3 : DGTP.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2J6U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1290030139. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI-111 DOUBLE CRYSTAL REMARK 200 OPTICS : PT-COATED MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17652 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 15.10 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.1 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.180 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2C22 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 25 MM TRIS-HCL PH 7.4, REMARK 280 100 MM CA(CH3CO2)2, 50MM NACL, 5 MM CACL2, 1 MM DGTP, AND 2.5% REMARK 280 GLYCEROL, PH 7.40 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 46.15900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.14250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.15900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.14250 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: 6470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, P, T 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 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 ALA A 346 REMARK 465 ILE A 347 REMARK 465 GLY A 348 REMARK 465 LEU A 349 REMARK 465 ASP A 350 REMARK 465 LYS A 351 REMARK 465 PHE A 352 REMARK 465 PHE A 353 REMARK 465 ASP A 354 REMARK 465 THR A 355 REMARK 465 DT T 1 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 GLU A 345 CA C O CB CG CD OE1 REMARK 470 GLU A 345 OE2 REMARK 470 DC T 2 P OP1 OP2 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 OD1 ASP A 108 O3' DT P 14 2.04 REMARK 500 O2 DT P 14 O HOH P 2019 2.09 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 DC T 4 C5' - C4' - C3' ANGL. DEV. = 7.8 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 HIS A 3 149.90 -177.28 REMARK 500 MET A 4 156.66 -45.87 REMARK 500 TYR A 13 55.66 22.89 REMARK 500 PHE A 14 -71.41 -33.94 REMARK 500 ASN A 23 72.49 -162.76 REMARK 500 GLU A 41 -61.68 0.54 REMARK 500 THR A 48 168.05 178.10 REMARK 500 SER A 99 136.25 175.99 REMARK 500 ASP A 108 22.02 -141.74 REMARK 500 ASP A 120 154.44 70.35 REMARK 500 SER A 148 -169.49 -169.47 REMARK 500 ASN A 164 57.31 32.54 REMARK 500 ASN A 237 45.42 -144.12 REMARK 500 ASP A 280 -109.98 68.07 REMARK 500 ASP A 295 40.39 -105.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DC T 4 0.09 SIDE CHAIN 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 ASP A 10 OD2 50.5 REMARK 620 3 ASP A 108 OD1 127.8 78.0 REMARK 620 4 GLU A 109 OE2 87.9 105.9 100.0 REMARK 620 5 DT P 14 O3' 165.5 115.3 39.5 100.6 REMARK 620 6 DGT P1016 O2A 97.7 85.1 84.4 168.8 76.1 REMARK 620 7 HOH P2022 O 73.2 118.7 155.5 92.6 117.7 79.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD2 REMARK 620 2 PHE A 11 O 97.9 REMARK 620 3 ASP A 108 OD2 68.0 75.3 REMARK 620 4 DGT P1016 O1B 143.6 83.6 77.5 REMARK 620 5 DGT P1016 O2G 114.9 118.0 164.7 95.6 REMARK 620 6 DGT P1016 O2A 94.1 139.9 74.2 65.0 90.5 REMARK 620 7 HOH P2026 O 80.1 75.5 132.6 134.3 61.6 144.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 184 O REMARK 620 2 ILE A 189 O 75.4 REMARK 620 3 HOH A2062 O 81.3 68.9 REMARK 620 4 HOH P2018 O 72.2 72.5 137.4 REMARK 620 5 HOH P2023 O 80.1 143.2 133.6 74.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGT P 1016 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JX4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX REMARK 900 WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE REMARK 900 RELATED ID: 1JXL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A Y-FAMILY DNA POLYMERASE IN A TERNARYCOMPLEX REMARK 900 WITH DNA SUBSTRATES AND AN INCOMING NUCLEOTIDE REMARK 900 RELATED ID: 1N48 RELATED DB: PDB REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC REMARK 900 LESION REMARK 900 RELATED ID: 1N56 RELATED DB: PDB REMARK 900 Y-FAMILY DNA POLYMERASE DPO4 IN COMPLEX WITH DNA CONTAININGABASIC REMARK 900 LESION REMARK 900 RELATED ID: 1RYR RELATED DB: PDB REMARK 900 REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION REMARK 900 RELATED ID: 1RYS RELATED DB: PDB REMARK 900 REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION REMARK 900 RELATED ID: 1S0M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A BENZO[A]PYRENE DIOL EPOXIDE ADDUCTIN A REMARK 900 TERNARY COMPLEX WITH A DNA POLYMERASE REMARK 900 RELATED ID: 1S0N RELATED DB: PDB REMARK 900 SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS REMARK 900 FOR BASE SUBSTITUTION AND FRAMESHIFT REMARK 900 RELATED ID: 1S0O RELATED DB: PDB REMARK 900 SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS REMARK 900 FOR BASE SUBSTITUTION AND FRAMESHIFT REMARK 900 RELATED ID: 1S10 RELATED DB: PDB REMARK 900 SNAPSHOTS OF REPLICATION THROUGH AN ABASIC LESION:STRUCTURAL BASIS REMARK 900 FOR BASE SUBSTITUTION AND FRAMESHIFT REMARK 900 RELATED ID: 1S97 RELATED DB: PDB REMARK 900 DPO4 WITH GT MISMATCH REMARK 900 RELATED ID: 1S9F RELATED DB: PDB REMARK 900 DPO WITH AT MATCHED REMARK 900 RELATED ID: 2AGO RELATED DB: PDB REMARK 900 FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND REMARK 900 PYROPHOSPHOROLYSIS REMARK 900 RELATED ID: 2AGP RELATED DB: PDB REMARK 900 FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND REMARK 900 PYROPHOSPHOROLYSIS REMARK 900 RELATED ID: 2AGQ RELATED DB: PDB REMARK 900 FIDELITY OF DPO4: EFFECT OF METAL IONS, NUCLEOTIDESELECTION AND REMARK 900 PYROPHOSPHOROLYSIS REMARK 900 RELATED ID: 2ASD RELATED DB: PDB REMARK 900 OXOG-MODIFIED INSERTION TERNARY COMPLEX REMARK 900 RELATED ID: 2ASJ RELATED DB: PDB REMARK 900 OXOG-MODIFIED PREINSERTION BINARY COMPLEX REMARK 900 RELATED ID: 2ASL RELATED DB: PDB REMARK 900 OXOG-MODIFIED POSTINSERTION BINARY COMPLEX REMARK 900 RELATED ID: 2ATL RELATED DB: PDB REMARK 900 UNMODIFIED INSERTION TERNARY COMPLEX REMARK 900 RELATED ID: 2AU0 RELATED DB: PDB REMARK 900 UNMODIFIED PREINSERTION BINARY COMPLEX REMARK 900 RELATED ID: 2BQ3 RELATED DB: PDB REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE REMARK 900 RELATED ID: 2BQR RELATED DB: PDB REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE REMARK 900 RELATED ID: 2BQU RELATED DB: PDB REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE REMARK 900 RELATED ID: 2BR0 RELATED DB: PDB REMARK 900 DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. REMARK 900 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION REMARK 900 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1 ,N2-ETHENOGUANINE REMARK 900 RELATED ID: 2C22 RELATED DB: PDB REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA REMARK 900 POLYMERASE DPO4 REMARK 900 RELATED ID: 2C28 RELATED DB: PDB REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA REMARK 900 POLYMERASE DPO4 REMARK 900 RELATED ID: 2C2D RELATED DB: PDB REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA REMARK 900 POLYMERASE DPO4 REMARK 900 RELATED ID: 2C2E RELATED DB: PDB REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA REMARK 900 POLYMERASE DPO4 REMARK 900 RELATED ID: 2C2R RELATED DB: PDB REMARK 900 EFFICIENT AND HIGH FIDELITY INCORPORATION OF DCTP OPPOSITE 7,8- REMARK 900 DIHYDRO-8- OXODEOXYGUANOSINE BY SULFOLOBUS SOLFATARICUS DNA REMARK 900 POLYMERASE DPO4 REMARK 900 RELATED ID: 2J6S RELATED DB: PDB REMARK 900 TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6- REMARK 900 METHYLGUANINE MODIFIED DNA, AND DATP. REMARK 900 RELATED ID: 2J6T RELATED DB: PDB REMARK 900 TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, O6- REMARK 900 METHYLGUANINE MODIFIED DNA, AND DATP. DBREF 2J6U A -2 3 PDB 2J6U 2J6U -2 3 DBREF 2J6U A 4 355 UNP Q97W02 DPO42_SULSO 1 352 DBREF 2J6U P 1 14 PDB 2J6U 2J6U 1 14 DBREF 2J6U T 1 18 PDB 2J6U 2J6U 1 18 SEQRES 1 A 358 HIS HIS HIS HIS HIS HIS MET ILE VAL LEU PHE VAL ASP SEQRES 2 A 358 PHE ASP TYR PHE TYR ALA GLN VAL GLU GLU VAL LEU ASN SEQRES 3 A 358 PRO SER LEU LYS GLY LYS PRO VAL VAL VAL CYS VAL PHE SEQRES 4 A 358 SER GLY ARG PHE GLU ASP SER GLY ALA VAL ALA THR ALA SEQRES 5 A 358 ASN TYR GLU ALA ARG LYS PHE GLY VAL LYS ALA GLY ILE SEQRES 6 A 358 PRO ILE VAL GLU ALA LYS LYS ILE LEU PRO ASN ALA VAL SEQRES 7 A 358 TYR LEU PRO MET ARG LYS GLU VAL TYR GLN GLN VAL SER SEQRES 8 A 358 SER ARG ILE MET ASN LEU LEU ARG GLU TYR SER GLU LYS SEQRES 9 A 358 ILE GLU ILE ALA SER ILE ASP GLU ALA TYR LEU ASP ILE SEQRES 10 A 358 SER ASP LYS VAL ARG ASP TYR ARG GLU ALA TYR ASN LEU SEQRES 11 A 358 GLY LEU GLU ILE LYS ASN LYS ILE LEU GLU LYS GLU LYS SEQRES 12 A 358 ILE THR VAL THR VAL GLY ILE SER LYS ASN LYS VAL PHE SEQRES 13 A 358 ALA LYS ILE ALA ALA ASP MET ALA LYS PRO ASN GLY ILE SEQRES 14 A 358 LYS VAL ILE ASP ASP GLU GLU VAL LYS ARG LEU ILE ARG SEQRES 15 A 358 GLU LEU ASP ILE ALA ASP VAL PRO GLY ILE GLY ASN ILE SEQRES 16 A 358 THR ALA GLU LYS LEU LYS LYS LEU GLY ILE ASN LYS LEU SEQRES 17 A 358 VAL ASP THR LEU SER ILE GLU PHE ASP LYS LEU LYS GLY SEQRES 18 A 358 MET ILE GLY GLU ALA LYS ALA LYS TYR LEU ILE SER LEU SEQRES 19 A 358 ALA ARG ASP GLU TYR ASN GLU PRO ILE ARG THR ARG VAL SEQRES 20 A 358 ARG LYS SER ILE GLY ARG ILE VAL THR MET LYS ARG ASN SEQRES 21 A 358 SER ARG ASN LEU GLU GLU ILE LYS PRO TYR LEU PHE ARG SEQRES 22 A 358 ALA ILE GLU GLU SER TYR TYR LYS LEU ASP LYS ARG ILE SEQRES 23 A 358 PRO LYS ALA ILE HIS VAL VAL ALA VAL THR GLU ASP LEU SEQRES 24 A 358 ASP ILE VAL SER ARG GLY ARG THR PHE PRO HIS GLY ILE SEQRES 25 A 358 SER LYS GLU THR ALA TYR SER GLU SER VAL LYS LEU LEU SEQRES 26 A 358 GLN LYS ILE LEU GLU GLU ASP GLU ARG LYS ILE ARG ARG SEQRES 27 A 358 ILE GLY VAL ARG PHE SER LYS PHE ILE GLU ALA ILE GLY SEQRES 28 A 358 LEU ASP LYS PHE PHE ASP THR SEQRES 1 P 14 DG DG DG DG DG DA DA DG DG DA DT DT DC SEQRES 2 P 14 DT SEQRES 1 T 18 DT DC DA DC 6OG DG DA DA DT DC DC DT DT SEQRES 2 T 18 DC DC DC DC DC MODRES 2J6U 6OG T 5 DG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HET 6OG T 5 23 HET CA A1001 1 HET CA A1002 1 HET CA A1003 1 HET DGT P1016 31 HETNAM 6OG 6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE FORMUL 3 6OG C11 H16 N5 O7 P FORMUL 4 CA 3(CA 2+) FORMUL 7 DGT C10 H16 N5 O13 P3 FORMUL 8 HOH *147(H2 O) HELIX 1 1 TYR A 13 LEU A 22 1 10 HELIX 2 2 ASN A 23 LYS A 27 5 5 HELIX 3 3 ASN A 50 LYS A 55 1 6 HELIX 4 4 PRO A 63 LEU A 71 1 9 HELIX 5 5 ARG A 80 GLU A 97 1 18 HELIX 6 6 ARG A 119 LYS A 140 1 22 HELIX 7 7 ASN A 150 LYS A 162 1 13 HELIX 8 8 ASP A 170 LEU A 181 1 12 HELIX 9 9 ILE A 183 VAL A 186 5 4 HELIX 10 10 GLY A 190 GLY A 201 1 12 HELIX 11 11 LEU A 205 ILE A 211 5 7 HELIX 12 12 GLU A 212 GLY A 221 1 10 HELIX 13 13 GLY A 221 ARG A 233 1 13 HELIX 14 14 ASN A 260 ASP A 280 1 21 HELIX 15 15 SER A 310 ASP A 329 1 20 SHEET 1 AA 5 ILE A 102 SER A 106 0 SHEET 2 AA 5 GLU A 109 ASP A 113 -1 O GLU A 109 N SER A 106 SHEET 3 AA 5 VAL A 6 PHE A 11 -1 O LEU A 7 N LEU A 112 SHEET 4 AA 5 VAL A 143 SER A 148 -1 O THR A 144 N ASP A 10 SHEET 5 AA 5 ILE A 166 VAL A 168 1 O LYS A 167 N ILE A 147 SHEET 1 AB 3 GLY A 44 ALA A 49 0 SHEET 2 AB 3 VAL A 31 PHE A 36 -1 O VAL A 33 N ALA A 47 SHEET 3 AB 3 VAL A 75 PRO A 78 1 O VAL A 75 N VAL A 32 SHEET 1 AC 4 SER A 247 SER A 258 0 SHEET 2 AC 4 ILE A 333 PHE A 343 -1 O ILE A 333 N SER A 258 SHEET 3 AC 4 PRO A 284 THR A 293 -1 N LYS A 285 O SER A 341 SHEET 4 AC 4 ILE A 298 THR A 304 -1 O VAL A 299 N ALA A 291 LINK O3' DC T 4 P 6OG T 5 1555 1555 1.61 LINK O3' 6OG T 5 P DG T 6 1555 1555 1.59 LINK OD1 ASP A 10 CA CA A1001 1555 1555 2.70 LINK OD2 ASP A 10 CA CA A1001 1555 1555 2.55 LINK OD2 ASP A 10 CA CA A1002 1555 1555 2.59 LINK O PHE A 11 CA CA A1002 1555 1555 2.48 LINK OD1 ASP A 108 CA CA A1001 1555 1555 3.03 LINK OD2 ASP A 108 CA CA A1002 1555 1555 2.64 LINK OE2 GLU A 109 CA CA A1001 1555 1555 2.63 LINK O ALA A 184 CA CA A1003 1555 1555 2.81 LINK O ILE A 189 CA CA A1003 1555 1555 2.85 LINK CA CA A1001 O3'A DT P 14 1555 1555 3.02 LINK CA CA A1001 O2A DGT P1016 1555 1555 2.75 LINK CA CA A1001 O HOH P2022 1555 1555 2.56 LINK CA CA A1002 O1B DGT P1016 1555 1555 2.59 LINK CA CA A1002 O2G DGT P1016 1555 1555 2.52 LINK CA CA A1002 O2A DGT P1016 1555 1555 2.31 LINK CA CA A1002 O HOH P2026 1555 1555 2.86 LINK CA CA A1003 O HOH A2062 1555 1555 2.68 LINK CA CA A1003 O HOH P2018 1555 1555 2.68 LINK CA CA A1003 O HOH P2023 1555 1555 2.87 CISPEP 1 LYS A 162 PRO A 163 0 -0.13 SITE 1 AC1 7 ASP A 10 ASP A 108 GLU A 109 CA A1002 SITE 2 AC1 7 DT P 14 DGT P1016 HOH P2022 SITE 1 AC2 6 ASP A 10 PHE A 11 ASP A 108 CA A1001 SITE 2 AC2 6 DGT P1016 HOH P2026 SITE 1 AC3 5 ALA A 184 ILE A 189 HOH A2062 HOH P2018 SITE 2 AC3 5 HOH P2023 SITE 1 AC4 23 ASP A 10 PHE A 11 ASP A 12 TYR A 13 SITE 2 AC4 23 PHE A 14 TYR A 15 ALA A 47 THR A 48 SITE 3 AC4 23 TYR A 51 ARG A 54 ASP A 108 LYS A 162 SITE 4 AC4 23 CA A1001 CA A1002 HOH A2023 HOH A2050 SITE 5 AC4 23 DT P 14 HOH P2019 HOH P2021 HOH P2025 SITE 6 AC4 23 HOH P2026 DC T 4 6OG T 5 CRYST1 92.318 102.285 52.485 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 0.010832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019053 0.00000