HEADER TRANSFERASE/DNA 22-MAR-10 3M9M TITLE CRYSTAL STRUCTURE OF DPO4 IN COMPLEX WITH DNA CONTAINING THE MAJOR TITLE 2 CISPLATIN LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IV; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: POL IV; COMPND 5 EC: 2.7.7.7; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*G)-3'); COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'- COMPND 13 D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'); COMPND 14 CHAIN: T; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 STRAIN: P2; SOURCE 5 GENE: DBH, DPO4, SSO2448; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B; 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 DPO4, TRANSLESION DNA SYNTHESIS, TLS, CISPLATIN, Y-FAMILY DNA KEYWDS 2 POLYMERASE, PROTEIN-DNA COMPLEX, DNA, DNA DAMAGE, DNA REPAIR, DNA KEYWDS 3 REPLICATION, DNA-BINDING, DNA-DIRECTED DNA POLYMERASE, MAGNESIUM, KEYWDS 4 METAL-BINDING, MUTATOR PROTEIN, NUCLEOTIDYLTRANSFERASE, TRANSFERASE, KEYWDS 5 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.H.Y.WONG,H.LING REVDAT 5 13-MAR-24 3M9M 1 SOURCE REVDAT 4 06-SEP-23 3M9M 1 REMARK LINK REVDAT 3 08-NOV-17 3M9M 1 REMARK REVDAT 2 07-JUL-10 3M9M 1 JRNL REVDAT 1 16-JUN-10 3M9M 0 JRNL AUTH J.H.WONG,J.A.BROWN,Z.SUO,P.BLUM,T.NOHMI,H.LING JRNL TITL STRUCTURAL INSIGHT INTO DYNAMIC BYPASS OF THE MAJOR JRNL TITL 2 CISPLATIN-DNA ADDUCT BY Y-FAMILY POLYMERASE DPO4. JRNL REF EMBO J. V. 29 2059 2010 JRNL REFN ISSN 0261-4189 JRNL PMID 20512114 JRNL DOI 10.1038/EMBOJ.2010.101 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 11987 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) : 0.285 REMARK 3 FREE R VALUE : 0.309 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.700 REMARK 3 FREE R VALUE TEST SET COUNT : 818 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2743 REMARK 3 NUCLEIC ACID ATOMS : 554 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.09200 REMARK 3 B22 (A**2) : 3.73900 REMARK 3 B33 (A**2) : 7.35300 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.510 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.452 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.641 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.918 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.451 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 32.47 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_JW_020210_GG1.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 5 : CTP_PAR_121707.TXT REMARK 3 PARAMETER FILE 6 : GOL_XPLOR_PAR.TXT REMARK 3 PARAMETER FILE 7 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3M9M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058281. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0781 REMARK 200 MONOCHROMATOR : CRYO-COOLED SI(111) DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC Q315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12009 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1JX4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M CALCIUM ACETATE, 5% GLYCEROL, 15% REMARK 280 PEG 3350, 200MM NACL, PH 7.5, HANGING DROP, TEMPERATURE 298K 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 49.28800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.59650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.28800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.59650 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: 5760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -89.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLU B 342 REMARK 465 ALA B 343 REMARK 465 ILE B 344 REMARK 465 GLY B 345 REMARK 465 LEU B 346 REMARK 465 ASP B 347 REMARK 465 LYS B 348 REMARK 465 PHE B 349 REMARK 465 PHE B 350 REMARK 465 ASP B 351 REMARK 465 THR B 352 REMARK 465 DT T 0 REMARK 465 DC T 1 REMARK 465 DT T 2 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 DG P 13 O5' C5' C4' O4' C3' O3' C2' REMARK 470 DG P 13 C1' N9 C8 N7 C5 C6 O6 REMARK 470 DG P 13 N1 C2 N2 N3 C4 REMARK 470 DC T 5 P 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 DG T 3 C2 DG T 3 N3 0.052 REMARK 500 DG T 3 N3 DG T 3 C4 0.081 REMARK 500 DG T 3 N7 DG T 3 C8 -0.095 REMARK 500 DG T 3 N9 DG T 3 C4 0.117 REMARK 500 DG T 4 C1' DG T 4 N9 0.121 REMARK 500 DG T 4 C5 DG T 4 C6 -0.100 REMARK 500 DG T 4 N7 DG T 4 C8 0.080 REMARK 500 DG T 4 C8 DG T 4 N9 0.106 REMARK 500 DG T 4 N9 DG T 4 C4 -0.116 REMARK 500 DC T 5 C5' DC T 5 C4' 0.085 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 DG P 13 O3' - P - OP2 ANGL. DEV. = 7.0 DEGREES REMARK 500 DG T 3 O4' - C1' - N9 ANGL. DEV. = -12.7 DEGREES REMARK 500 DG T 3 C2 - N3 - C4 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG T 3 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 DG T 3 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG T 3 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG T 3 N9 - C4 - C5 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG T 3 N3 - C4 - N9 ANGL. DEV. = 9.3 DEGREES REMARK 500 DG T 3 C8 - N9 - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 DG T 4 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG T 4 C4 - C5 - N7 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG T 4 N7 - C8 - N9 ANGL. DEV. = -4.0 DEGREES REMARK 500 DG T 4 C6 - C5 - N7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DG T 4 C8 - N9 - C1' ANGL. DEV. = 9.2 DEGREES REMARK 500 DG T 4 C4 - N9 - C1' ANGL. DEV. = -10.1 DEGREES REMARK 500 DT T 11 C3' - C2' - C1' ANGL. DEV. = -6.3 DEGREES REMARK 500 DC T 16 O5' - C5' - C4' ANGL. DEV. = -7.5 DEGREES REMARK 500 DC T 17 C1' - O4' - C4' ANGL. DEV. = -6.1 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 B 10 45.98 16.53 REMARK 500 PHE B 11 -78.81 -29.71 REMARK 500 VAL B 15 -2.33 -55.93 REMARK 500 ASN B 20 70.79 -164.77 REMARK 500 PHE B 37 159.22 156.49 REMARK 500 ASN B 47 167.95 -46.33 REMARK 500 LYS B 52 -19.91 -48.71 REMARK 500 SER B 96 141.58 170.68 REMARK 500 ASP B 105 35.59 -151.75 REMARK 500 ILE B 111 46.97 -105.52 REMARK 500 ASP B 113 17.72 -142.15 REMARK 500 SER B 145 -168.19 -173.16 REMARK 500 ASN B 161 57.80 35.82 REMARK 500 ILE B 166 76.83 -115.72 REMARK 500 VAL B 203 -18.64 -49.44 REMARK 500 ASP B 211 -16.12 -48.97 REMARK 500 ARG B 253 140.87 -176.14 REMARK 500 SER B 255 166.41 175.82 REMARK 500 ASP B 277 89.81 40.32 REMARK 500 LYS B 278 -18.17 81.25 REMARK 500 THR B 290 156.38 -48.27 REMARK 500 PHE B 340 -179.41 -61.13 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 DG T 3 0.12 SIDE CHAIN REMARK 500 DG T 4 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CTP B 2001 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 B 354 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 7 OD1 REMARK 620 2 PHE B 8 O 83.4 REMARK 620 3 ASP B 105 OD2 116.0 82.4 REMARK 620 4 CTP B2001 O2B 153.1 92.5 89.5 REMARK 620 5 CTP B2001 O1A 109.6 155.3 108.6 66.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 353 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 105 OD1 REMARK 620 2 GLU B 106 OE2 108.6 REMARK 620 3 CTP B2001 O5' 89.1 161.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 355 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 181 O REMARK 620 2 ILE B 186 O 75.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT T1004 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 3 N7 REMARK 620 2 CPT T1004 N1 175.0 REMARK 620 3 CPT T1004 N2 86.5 89.2 REMARK 620 4 DG T 4 N7 99.5 84.7 172.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTP B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 355 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 356 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 357 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL P 14 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL P 15 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT T 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3M9N RELATED DB: PDB REMARK 900 RELATED ID: 3M9O RELATED DB: PDB DBREF 3M9M B 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 3M9M P 1 13 PDB 3M9M 3M9M 1 13 DBREF 3M9M T 0 17 PDB 3M9M 3M9M 0 17 SEQRES 1 B 352 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 B 352 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 B 352 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 B 352 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 B 352 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 B 352 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 B 352 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 B 352 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 B 352 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 B 352 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 B 352 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 B 352 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 B 352 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 B 352 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 B 352 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 B 352 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 B 352 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 B 352 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 B 352 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 B 352 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 B 352 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 B 352 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 B 352 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 B 352 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 B 352 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 B 352 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 B 352 LYS PHE ILE GLU ALA ILE GLY LEU ASP LYS PHE PHE ASP SEQRES 28 B 352 THR SEQRES 1 P 13 DG DG DG DG DG DA DA DG DG DA DA DA DG SEQRES 1 T 18 DT DC DT DG DG DC DT DT DT DC DC DT DT SEQRES 2 T 18 DC DC DC DC DC HET CTP B2001 28 HET CA B 353 1 HET CA B 354 1 HET CA B 355 1 HET CA B 356 1 HET GOL B 357 6 HET GOL P 14 6 HET GOL P 15 6 HET CPT T1004 3 HETNAM CTP CYTIDINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM CPT CISPLATIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 4 CTP C9 H16 N3 O14 P3 FORMUL 5 CA 4(CA 2+) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 12 CPT CL2 H6 N2 PT FORMUL 13 HOH *51(H2 O) HELIX 1 1 TYR B 10 VAL B 18 1 9 HELIX 2 2 ASN B 20 LYS B 24 5 5 HELIX 3 3 ASN B 47 LYS B 52 1 6 HELIX 4 4 PRO B 60 LEU B 68 1 9 HELIX 5 5 ARG B 77 ARG B 93 1 17 HELIX 6 6 ASP B 117 LYS B 137 1 21 HELIX 7 7 ASN B 147 LYS B 159 1 13 HELIX 8 8 ASP B 167 LEU B 178 1 12 HELIX 9 9 ASP B 179 VAL B 183 5 5 HELIX 10 10 GLY B 187 LYS B 196 1 10 HELIX 11 11 LYS B 201 LEU B 206 5 6 HELIX 12 12 PHE B 210 GLY B 215 1 6 HELIX 13 13 GLY B 218 ARG B 230 1 13 HELIX 14 14 ASN B 257 ASP B 277 1 21 HELIX 15 15 SER B 307 ASP B 326 1 20 SHEET 1 A 5 ILE B 99 SER B 103 0 SHEET 2 A 5 GLU B 106 ASP B 110 -1 O TYR B 108 N GLU B 100 SHEET 3 A 5 VAL B 3 PHE B 8 -1 N LEU B 4 O LEU B 109 SHEET 4 A 5 VAL B 140 SER B 145 -1 O SER B 145 N VAL B 3 SHEET 5 A 5 ILE B 163 VAL B 165 1 O LYS B 164 N ILE B 144 SHEET 1 B 3 GLY B 41 ALA B 46 0 SHEET 2 B 3 VAL B 28 PHE B 33 -1 N VAL B 32 O ALA B 42 SHEET 3 B 3 VAL B 72 PRO B 75 1 O LEU B 74 N CYS B 31 SHEET 1 C 4 ILE B 245 SER B 255 0 SHEET 2 C 4 ILE B 330 PHE B 340 -1 O ILE B 333 N VAL B 249 SHEET 3 C 4 PRO B 281 THR B 290 -1 N ALA B 283 O SER B 338 SHEET 4 C 4 ILE B 295 THR B 301 -1 O ARG B 298 N VAL B 286 LINK OD1 ASP B 7 CA CA B 354 1555 1555 2.33 LINK O PHE B 8 CA CA B 354 1555 1555 2.49 LINK OD1 ASP B 105 CA CA B 353 1555 1555 3.09 LINK OD2 ASP B 105 CA CA B 354 1555 1555 2.57 LINK OE2 GLU B 106 CA CA B 353 1555 1555 2.76 LINK O ALA B 181 CA CA B 355 1555 1555 2.74 LINK O ILE B 186 CA CA B 355 1555 1555 2.82 LINK CA CA B 353 O5' CTP B2001 1555 1555 2.99 LINK CA CA B 354 O2B CTP B2001 1555 1555 2.53 LINK CA CA B 354 O1A CTP B2001 1555 1555 3.14 LINK N7 DG T 3 PT1 CPT T1004 1555 1555 1.97 LINK N7 DG T 4 PT1 CPT T1004 1555 1555 1.94 CISPEP 1 LYS B 159 PRO B 160 0 0.00 SITE 1 AC1 17 PHE B 8 ASP B 9 TYR B 10 PHE B 11 SITE 2 AC1 17 TYR B 12 THR B 45 TYR B 48 ARG B 51 SITE 3 AC1 17 ALA B 57 ASP B 105 LYS B 159 CA B 353 SITE 4 AC1 17 CA B 354 HOH B 377 HOH B 378 HOH B 379 SITE 5 AC1 17 DG T 4 SITE 1 AC2 4 ASP B 105 GLU B 106 CA B 354 CTP B2001 SITE 1 AC3 5 ASP B 7 PHE B 8 ASP B 105 CA B 353 SITE 2 AC3 5 CTP B2001 SITE 1 AC4 2 ALA B 181 ILE B 186 SITE 1 AC5 1 ASP B 156 SITE 1 AC6 2 GLY B 185 DC T 10 SITE 1 AC7 3 DG P 2 DG P 3 DG P 4 SITE 1 AC8 3 DA P 6 DA P 7 DC T 13 SITE 1 AC9 2 DG T 3 DG T 4 CRYST1 98.576 101.193 52.418 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 0.010144 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019077 0.00000