HEADER TRANSFERASE 27-APR-05 2BQR TITLE DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS DPO4. TITLE 2 ANALYSIS AND CRYSTAL STRUCTURES OF MULTIPLE BASE-PAIR SUBSTITUTION TITLE 3 AND FRAMESHIFT PRODUCTS WITH THE ADDUCT 1,N2-ETHENOGUANINE 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*C)-3'; COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP COMPND 13 *TP*TP*CP*CP*CP*CP*C)-3'; COMPND 14 CHAIN: T; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: 18-MER DNA TEMPLATE CONTAINING 1, N2-ETHENOGUANINE COMPND 17 ADDUCT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_COMMON: SULFOLOBUS FATARICUS; SOURCE 4 ORGANISM_TAXID: 273057; SOURCE 5 STRAIN: P2; SOURCE 6 GENE: DPO4; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22B/DPO4-NHIS; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES KEYWDS P2 DNA POLYMERASE IV, 1N2-ETHENOGUANINE ADDUCT, TRANSLESION DNA KEYWDS 2 POLYMERASE, DATP, NUCLEOTIDYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.IRIMIA,L.V.LOUKACHEVITCH,M.EGLI REVDAT 4 13-DEC-23 2BQR 1 LINK REVDAT 3 24-FEB-09 2BQR 1 VERSN REVDAT 2 17-AUG-05 2BQR 1 JRNL REVDAT 1 23-JUN-05 2BQR 0 JRNL AUTH H.ZANG,A.K.GOODENOUGH,J.Y.CHOI,A.IRIMIA,L.V.LOUKACHEVITCH, JRNL AUTH 2 I.D.KOZEKOV,K.C.ANGEL,C.J.RIZZO,M.EGLI,F.P.GUENGERICH JRNL TITL DNA ADDUCT BYPASS POLYMERIZATION BY SULFOLOBUS SOLFATARICUS JRNL TITL 2 DNA POLYMERASE DPO4: ANALYSIS AND CRYSTAL STRUCTURES OF JRNL TITL 3 MULTIPLE BASE PAIR SUBSTITUTION AND FRAMESHIFT PRODUCTS WITH JRNL TITL 4 THE ADDUCT 1,N2-ETHENOGUANINE. JRNL REF J.BIOL.CHEM. V. 280 29750 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15965231 JRNL DOI 10.1074/JBC.M504756200 REMARK 2 REMARK 2 RESOLUTION. 2.37 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) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1324284.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 20350 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) : 0.223 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 998 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2254 REMARK 3 BIN R VALUE (WORKING SET) : 0.4070 REMARK 3 BIN FREE R VALUE : 0.4170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 119 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2744 REMARK 3 NUCLEIC ACID ATOMS : 611 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.20000 REMARK 3 B22 (A**2) : -5.38000 REMARK 3 B33 (A**2) : 1.18000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.40 REMARK 3 LOW RESOLUTION CUTOFF (A) : 42.3 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.970 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) : 1.370 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.340 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.350 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 44.13 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : ATP.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : ATP.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FIRST NUCLEOTIDE OF THE TEMPLATE REMARK 3 DNA IS NOT OBSERVED IN THE STRUCTURE. REMARK 4 REMARK 4 2BQR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.991 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH MAR300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20350 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 42.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 65.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2BQ3 REMARK 200 REMARK 200 REMARK: THE STARTING MODEL WAS THE PDB FILE WITH THE ACCESSION REMARK 200 CODE 2BQ3. ITS POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID REMARK 200 BODY REFINEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 3350, 0.1 M HEPES PH 7.0, 100 REMARK 280 MM CALCIUM ACETATE, 2.5% GLYCEROL, 0.5 MM DATP, PH 7.00 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 47.76400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.51350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.76400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.51350 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: PQS 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 -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 GLU A 342 REMARK 465 ALA A 343 REMARK 465 ILE A 344 REMARK 465 GLY A 345 REMARK 465 LEU A 346 REMARK 465 ASP A 347 REMARK 465 LYS A 348 REMARK 465 PHE A 349 REMARK 465 PHE A 350 REMARK 465 ASP A 351 REMARK 465 THR A 352 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 DC T 2 P OP1 OP2 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 4 C3' - O3' - P ANGL. DEV. = -19.3 DEGREES REMARK 500 GNE T 5 C3' - O3' - P ANGL. DEV. = -21.5 DEGREES REMARK 500 DG T 6 O3' - P - OP2 ANGL. DEV. = 8.3 DEGREES REMARK 500 DG T 6 O3' - P - OP1 ANGL. DEV. = -14.5 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 TYR A 10 52.98 19.31 REMARK 500 PRO A 21 -19.71 -49.75 REMARK 500 SER A 22 2.06 -69.45 REMARK 500 ARG A 36 -107.46 -68.85 REMARK 500 SER A 96 132.31 -179.39 REMARK 500 SER A 96 133.59 -179.39 REMARK 500 ASP A 105 23.24 -146.89 REMARK 500 ILE A 111 51.32 -105.72 REMARK 500 LYS A 137 31.70 70.81 REMARK 500 ASN A 161 41.99 38.43 REMARK 500 PHE A 210 -39.58 -36.97 REMARK 500 PHE A 210 -39.58 -32.61 REMARK 500 ASN A 234 55.97 -147.56 REMARK 500 ASP A 277 88.62 27.27 REMARK 500 LYS A 278 -23.28 85.54 REMARK 500 ASP A 292 41.67 -105.34 REMARK 500 ARG A 300 129.91 -173.15 REMARK 500 ASP A 326 115.03 -165.84 REMARK 500 LYS A 339 62.35 60.04 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 DT T 4 0.07 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 A2001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 ASP A 7 OD2 38.7 REMARK 620 3 ASP A 105 OD2 62.0 97.5 REMARK 620 4 ASP A 105 OD1 98.2 125.0 39.4 REMARK 620 5 GLU A 106 OE2 110.9 77.3 127.9 102.7 REMARK 620 6 DTP A1000 O1A 122.9 121.7 116.2 110.1 109.7 REMARK 620 7 DTP A1000 O3A 80.7 101.5 80.4 100.9 151.7 46.5 REMARK 620 8 DTP A1000 O5' 117.9 149.8 74.4 65.9 130.9 45.9 48.9 REMARK 620 9 CA A2002 CA 43.3 79.5 44.0 81.0 153.7 92.8 46.5 74.6 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 85.7 REMARK 620 3 ASP A 105 OD2 88.2 89.4 REMARK 620 4 DTP A1000 O2B 97.1 98.5 170.8 REMARK 620 5 DTP A1000 O3G 177.6 95.9 93.6 80.9 REMARK 620 6 DTP A1000 O3A 116.9 147.6 112.8 58.0 60.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 181 O REMARK 620 2 ILE A 186 O 88.3 REMARK 620 3 HOH A2004 O 98.6 161.0 REMARK 620 4 HOH A2007 O 91.2 137.4 60.6 REMARK 620 5 HOH A2043 O 93.0 71.0 125.8 66.4 REMARK 620 6 HOH P2016 O 92.6 74.2 87.7 148.3 144.6 REMARK 620 7 HOH P2017 O 171.2 83.6 90.2 92.4 81.0 88.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A2003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP A1000 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: 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: 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 999 REMARK 999 SEQUENCE REMARK 999 THE FIRST NUCLEOTIDE OF THE TEMPLATE DNA IS NOT OBSERVED REMARK 999 IN THE STRUCTURE. DBREF 2BQR A -5 0 PDB 2BQR 2BQR -5 0 DBREF 2BQR A 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 2BQR P 1 13 PDB 2BQR 2BQR 1 13 DBREF 2BQR T 1 18 PDB 2BQR 2BQR 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 13 DG DG DG DG DG DA DA DG DG DA DT DT DC SEQRES 1 T 18 DT DC DA DT GNE DG DA DA DT DC DC DT DT SEQRES 2 T 18 DC DC DC DC DC HET GNE T 5 24 HET DTP A1000 30 HET CA A2001 1 HET CA A2002 1 HET CA A2003 1 HETNAM GNE 1,N2-ETHENOGUANINE HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 3 GNE C12 H14 N5 O7 P FORMUL 4 DTP C10 H16 N5 O12 P3 FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *109(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 PRO A 21 LYS A 24 5 4 HELIX 3 3 ASN A 47 LYS A 52 1 6 HELIX 4 4 PRO A 60 LEU A 68 1 9 HELIX 5 5 ARG A 77 GLU A 94 1 18 HELIX 6 6 ASP A 117 GLU A 136 1 20 HELIX 7 7 ASN A 147 LYS A 159 1 13 HELIX 8 8 ASP A 167 LEU A 178 1 12 HELIX 9 9 ILE A 180 VAL A 183 5 4 HELIX 10 10 GLY A 187 LEU A 197 1 11 HELIX 11 11 LEU A 202 ILE A 208 5 7 HELIX 12 12 GLU A 209 GLY A 218 1 10 HELIX 13 13 GLY A 218 ARG A 230 1 13 HELIX 14 14 ASN A 257 ASP A 277 1 21 HELIX 15 15 SER A 307 GLU A 325 1 19 SHEET 1 AA 5 ILE A 99 SER A 103 0 SHEET 2 AA 5 GLU A 106 ASP A 110 -1 O GLU A 106 N SER A 103 SHEET 3 AA 5 VAL A 3 PHE A 8 -1 O LEU A 4 N LEU A 109 SHEET 4 AA 5 VAL A 140 SER A 145 -1 O THR A 141 N ASP A 7 SHEET 5 AA 5 ILE A 163 VAL A 165 1 O LYS A 164 N ILE A 144 SHEET 1 AB 3 GLY A 41 ALA A 46 0 SHEET 2 AB 3 VAL A 28 PHE A 33 -1 O VAL A 30 N ALA A 44 SHEET 3 AB 3 VAL A 72 PRO A 75 1 O VAL A 72 N VAL A 29 SHEET 1 AC 4 SER A 244 SER A 255 0 SHEET 2 AC 4 ILE A 330 PHE A 340 -1 O ILE A 330 N SER A 255 SHEET 3 AC 4 PRO A 281 THR A 290 -1 N LYS A 282 O LYS A 339 SHEET 4 AC 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288 LINK O3' DT T 4 P GNE T 5 1555 1555 1.66 LINK O3' GNE T 5 P DG T 6 1555 1555 1.66 LINK OD1 ASP A 7 CA CA A2001 1555 1555 3.40 LINK OD2 ASP A 7 CA CA A2001 1555 1555 3.15 LINK OD1 ASP A 7 CA CA A2002 1555 1555 2.47 LINK O PHE A 8 CA CA A2002 1555 1555 2.33 LINK OD2 ASP A 105 CA CA A2001 1555 1555 3.26 LINK OD1 ASP A 105 CA CA A2001 1555 1555 3.26 LINK OD2 ASP A 105 CA CA A2002 1555 1555 2.46 LINK OE2 GLU A 106 CA CA A2001 1555 1555 2.99 LINK O ALA A 181 CA CA A2003 1555 1555 2.42 LINK O ILE A 186 CA CA A2003 1555 1555 2.64 LINK O1A DTP A1000 CA CA A2001 1555 1555 3.35 LINK O3A DTP A1000 CA CA A2001 1555 1555 3.25 LINK O5' DTP A1000 CA CA A2001 1555 1555 3.07 LINK O2B DTP A1000 CA CA A2002 1555 1555 2.60 LINK O3G DTP A1000 CA CA A2002 1555 1555 2.81 LINK O3A DTP A1000 CA CA A2002 1555 1555 2.59 LINK CA CA A2001 CA CA A2002 1555 1555 3.29 LINK CA CA A2001 O HOH A2029 1555 1555 3.01 LINK CA CA A2003 O HOH A2004 1555 1555 2.84 LINK CA CA A2003 O HOH A2007 1555 1555 2.82 LINK CA CA A2003 O HOH A2043 1555 1555 2.54 LINK CA CA A2003 O HOH P2016 1555 1555 2.47 LINK CA CA A2003 O HOH P2017 1555 1555 2.68 CISPEP 1 LYS A 159 PRO A 160 0 0.08 SITE 1 AC1 6 ASP A 7 ASP A 105 GLU A 106 DTP A1000 SITE 2 AC1 6 CA A2002 HOH A2029 SITE 1 AC2 5 ASP A 7 PHE A 8 ASP A 105 DTP A1000 SITE 2 AC2 5 CA A2001 SITE 1 AC3 7 ALA A 181 ILE A 186 HOH A2004 HOH A2007 SITE 2 AC3 7 HOH A2043 HOH P2016 HOH P2017 SITE 1 AC4 17 TYR A 10 PHE A 11 TYR A 12 ALA A 44 SITE 2 AC4 17 THR A 45 ARG A 51 ASP A 105 LYS A 159 SITE 3 AC4 17 CA A2001 CA A2002 HOH A2070 HOH A2071 SITE 4 AC4 17 HOH A2072 HOH A2073 HOH P2018 DT T 4 SITE 5 AC4 17 GNE T 5 CRYST1 95.528 103.027 53.097 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 0.010468 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018833 0.00000