HEADER TRANSFERASE 28-APR-05 2BQU 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 OTHER_DETAILS: 13-MER DNA PRIMER; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*TP*CP*AP*TP*GNEP*GP*AP*AP*TP*CP*CP COMPND 14 *TP*TP*CP*CP*CP*CP*C)-3'; COMPND 15 CHAIN: T; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: 18-MER TEMPLATE CONTAINING 1, N2-ETHENOGUANINE 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, DDATP, NUCLEOTIDYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.IRIMIA,L.V.LOUKACHEVITCH,M.EGLI REVDAT 4 13-DEC-23 2BQU 1 LINK REVDAT 3 24-FEB-09 2BQU 1 VERSN REVDAT 2 17-AUG-05 2BQU 1 JRNL REVDAT 1 23-JUN-05 2BQU 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. 2.50 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) : 42.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 949887.230 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 16976 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) : 0.221 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 828 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) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2154 REMARK 3 BIN R VALUE (WORKING SET) : 0.3850 REMARK 3 BIN FREE R VALUE : 0.4250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 106 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 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 : 32 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.97000 REMARK 3 B22 (A**2) : -6.31000 REMARK 3 B33 (A**2) : -0.66000 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) : 0.37 REMARK 3 LOW RESOLUTION CUTOFF (A) : 45.3 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) : 0.36 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) : 1.000 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) : 2.320 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.260 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 40.88 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 : DAD.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 : DAD.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 2BQU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-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) : 0.999 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 : 17022 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 42.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2000 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) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.7 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 PDB WITH ACCESSION CODE 2BQ3 SERVED AS STARTING MODEL. REMARK 200 THE MODEL POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REMARK 200 REFINEMENT. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 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 DDATP, 2.5 MM MGCL2, REMARK 280 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 47.67950 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 47.67950 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 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 GLU A 342 CA C O CB CG CD OE1 REMARK 470 GLU A 342 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 ND1 HIS A 285 O HOH A 2067 1.91 REMARK 500 OG SER A 34 O HOH A 2009 1.97 REMARK 500 OE2 GLU A 314 O HOH A 2075 2.01 REMARK 500 OE1 GLN A 82 O HOH A 2018 2.04 REMARK 500 OP1 DC T 11 O HOH T 2009 2.06 REMARK 500 O HOH A 2017 O HOH A 2018 2.12 REMARK 500 O HOH A 2004 O HOH A 2073 2.19 REMARK 500 O4 DT P 11 O HOH P 2013 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DT T 4 O3' DT T 4 C3' -0.073 REMARK 500 GNE T 5 O3' DG T 6 P -0.078 REMARK 500 DG T 6 P DG T 6 O5' 0.097 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 ARG A 173 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DT T 4 C3' - O3' - P ANGL. DEV. = 23.0 DEGREES REMARK 500 GNE T 5 O3' - P - O5' ANGL. DEV. = -18.6 DEGREES REMARK 500 GNE T 5 O3' - P - OP1 ANGL. DEV. = 7.9 DEGREES REMARK 500 DG T 6 O3' - P - OP1 ANGL. DEV. = 13.7 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 50.45 21.83 REMARK 500 ASN A 20 81.31 -157.95 REMARK 500 ASP A 168 -28.59 -39.87 REMARK 500 ASP A 168 -28.55 -39.87 REMARK 500 SER A 255 160.49 179.20 REMARK 500 ASP A 277 84.98 22.00 REMARK 500 LYS A 278 -24.19 85.57 REMARK 500 ASP A 292 33.27 -92.99 REMARK 500 ASP A 326 118.21 -164.92 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 A1343 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 ASP A 7 OD2 43.7 REMARK 620 3 ASP A 105 OD2 68.5 111.8 REMARK 620 4 GLU A 106 OE1 132.2 105.2 117.4 REMARK 620 5 DAD A1342 O3A 122.9 115.4 104.9 102.1 REMARK 620 6 DAD A1342 O5' 147.6 160.2 84.2 75.5 46.7 REMARK 620 7 CA A1344 CA 47.7 81.9 50.1 167.5 83.4 101.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1344 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 7 OD1 REMARK 620 2 PHE A 8 O 77.7 REMARK 620 3 ASP A 105 OD2 85.1 84.5 REMARK 620 4 DAD A1342 O3B 145.8 135.5 90.0 REMARK 620 5 DAD A1342 O2B 107.2 147.4 127.6 51.4 REMARK 620 6 DAD A1342 O1G 160.3 83.6 87.0 52.0 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1345 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 181 O REMARK 620 2 ILE A 186 O 72.3 REMARK 620 3 HOH A2045 O 99.1 76.5 REMARK 620 4 HOH P2006 O 106.8 134.4 144.4 REMARK 620 5 HOH P2014 O 142.6 72.8 85.4 88.4 REMARK 620 6 HOH P2015 O 69.6 58.8 135.3 77.8 81.1 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 CA A1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAD A1342 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: 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 DBREF 2BQU A -5 0 PDB 2BQU 2BQU -5 0 DBREF 2BQU A 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 2BQU P 1 13 PDB 2BQU 2BQU 1 13 DBREF 2BQU T 1 18 PDB 2BQU 2BQU 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 DAD A1342 29 HET CA A1343 1 HET CA A1344 1 HET CA A1345 1 HETNAM GNE 1,N2-ETHENOGUANINE HETNAM DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION FORMUL 3 GNE C12 H14 N5 O7 P FORMUL 4 DAD C10 H16 N5 O11 P3 FORMUL 5 CA 3(CA 2+) FORMUL 8 HOH *116(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 ARG A 119 LYS A 137 1 19 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 LYS A 196 1 10 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 ASP A 231 1 14 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 ILE A 166 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 1.60 LINK O3' GNE T 5 P DG T 6 1555 1555 1.53 LINK OD1 ASP A 7 CA CA A1343 1555 1555 3.08 LINK OD2 ASP A 7 CA CA A1343 1555 1555 2.82 LINK OD1 ASP A 7 CA CA A1344 1555 1555 2.50 LINK O PHE A 8 CA CA A1344 1555 1555 2.57 LINK OD2 ASP A 105 CA CA A1343 1555 1555 3.04 LINK OD2 ASP A 105 CA CA A1344 1555 1555 2.60 LINK OE1 GLU A 106 CA CA A1343 1555 1555 2.65 LINK O ALA A 181 CA CA A1345 1555 1555 2.54 LINK O ILE A 186 CA CA A1345 1555 1555 3.04 LINK O3A DAD A1342 CA CA A1343 1555 1555 2.87 LINK O5' DAD A1342 CA CA A1343 1555 1555 3.40 LINK O3B DAD A1342 CA CA A1344 1555 1555 3.06 LINK O2B DAD A1342 CA CA A1344 1555 1555 2.86 LINK O1G DAD A1342 CA CA A1344 1555 1555 2.90 LINK CA CA A1343 CA CA A1344 1555 1555 3.10 LINK CA CA A1345 O HOH A2045 1555 1555 2.52 LINK CA CA A1345 O HOH P2006 1555 1555 2.67 LINK CA CA A1345 O HOH P2014 1555 1555 2.39 LINK CA CA A1345 O HOH P2015 1555 1555 2.64 CISPEP 1 LYS A 159 PRO A 160 0 0.00 SITE 1 AC1 5 ASP A 7 ASP A 105 GLU A 106 DAD A1342 SITE 2 AC1 5 CA A1344 SITE 1 AC2 5 ASP A 7 PHE A 8 ASP A 105 DAD A1342 SITE 2 AC2 5 CA A1343 SITE 1 AC3 6 ALA A 181 ILE A 186 HOH A2045 HOH P2006 SITE 2 AC3 6 HOH P2014 HOH P2015 SITE 1 AC4 20 PHE A 8 TYR A 10 PHE A 11 TYR A 12 SITE 2 AC4 20 ALA A 44 THR A 45 ARG A 51 ASP A 105 SITE 3 AC4 20 LYS A 159 CA A1343 CA A1344 HOH A2084 SITE 4 AC4 20 HOH A2085 HOH A2086 HOH A2087 HOH A2088 SITE 5 AC4 20 HOH A2090 DC P 13 DT T 4 GNE T 5 CRYST1 95.359 103.027 52.987 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 0.010487 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009706 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018873 0.00000