HEADER TRANSFERASE/DNA/INHIBITOR 05-FEB-12 4DL5 TITLE HUMAN DNA POLYMERASE ETA INSERTING DCMPNPP OPPOSITE THE 5'G OF TITLE 2 CISPLATIN CROSSLINKED GS (PT-GG2). COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE ETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-432; COMPND 5 SYNONYM: RAD30 HOMOLOG A, XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*TP*AP*CP*GP*GP*TP*CP*AP*CP*AP*CP*T)-3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(P*TP*AP*GP*TP*GP*TP*GP*AP*C)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: DCMPNPP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLH, RAD30, RAD30A, XPV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS CISPLATIN, CHEMORESISTENCE, TRANSLESION SYNTHESIS, HUMAN DNA KEYWDS 2 POLYMERSE ETA, KINETICS, MOLECULAR SPLINT, INHIBITION, DNA KEYWDS 3 DISTORSION, SECOND TLS POLYMERASE, NUCLEOTIDYL TRANSFER REACTION, KEYWDS 4 PCNA, TRANSFERASE-DNA-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,C.BIERTUMPFEL,M.GREGORY,F.HANAOKA,Y.HUA,W.YANG REVDAT 4 13-SEP-23 4DL5 1 REMARK SEQADV LINK REVDAT 3 08-OCT-14 4DL5 1 AUTHOR REVDAT 2 26-JUN-13 4DL5 1 JRNL REVDAT 1 09-MAY-12 4DL5 0 JRNL AUTH Y.ZHAO,C.BIERTUMPFEL,M.T.GREGORY,Y.J.HUA,F.HANAOKA,W.YANG JRNL TITL STRUCTURAL BASIS FOR CHEMORESISTANCE TO CISPLATIN MEDIATED JRNL TITL 2 BY DNA POLYMERASE ETA JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 7269 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22529383 JRNL DOI 10.1073/PNAS.1202681109 REMARK 2 REMARK 2 RESOLUTION. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10046 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.245 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.540 REMARK 3 FREE R VALUE TEST SET COUNT : 757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9625 - 4.9731 1.00 1882 161 0.2304 0.2445 REMARK 3 2 4.9731 - 3.9574 1.00 1873 137 0.2204 0.2220 REMARK 3 3 3.9574 - 3.4601 1.00 1846 170 0.2374 0.2623 REMARK 3 4 3.4601 - 3.1451 1.00 1843 142 0.2836 0.2729 REMARK 3 5 3.1451 - 2.9204 1.00 1845 147 0.3475 0.3644 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 48.24 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.690 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.35460 REMARK 3 B22 (A**2) : -12.35460 REMARK 3 B33 (A**2) : 10.60620 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 4254 REMARK 3 ANGLE : 1.635 5905 REMARK 3 CHIRALITY : 0.099 665 REMARK 3 PLANARITY : 0.006 633 REMARK 3 DIHEDRAL : 21.177 1674 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4DL5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070466. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE SI(220) CRYSTAL AND REMARK 200 MIRROR VERTICAL FOCUSING REMARK 200 OPTICS : DOUBLE SI(220) CRYSTAL AND REMARK 200 MIRROR VERTICAL FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10069 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.920 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : 0.07600 REMARK 200 FOR THE DATA SET : 18.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.73000 REMARK 200 R SYM FOR SHELL (I) : 0.69400 REMARK 200 FOR SHELL : 2.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3MR2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, MGCL2, PEG 2K-MME, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.36167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.72333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.04250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.40417 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.68083 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: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLY A -2 REMARK 465 PRO A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 154 REMARK 465 THR A 155 REMARK 465 THR A 156 REMARK 465 ALA A 157 REMARK 465 GLY A 410 REMARK 465 ILE A 411 REMARK 465 GLN A 412 REMARK 465 DT T 1 REMARK 465 DA T 2 REMARK 465 DC T 3 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 VAL A 108 CG1 CG2 REMARK 470 GLU A 127 CG CD OE1 OE2 REMARK 470 LEU A 132 CG CD1 CD2 REMARK 470 GLN A 133 CG CD OE1 NE2 REMARK 470 GLU A 158 CG CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 GLN A 169 CG CD OE1 NE2 REMARK 470 LEU A 183 CG CD1 CD2 REMARK 470 THR A 184 OG1 CG2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 LEU A 378 CG CD1 CD2 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 6 C1' DT T 6 N1 -0.215 REMARK 500 DG P 7 O4' DG P 7 C1' -0.073 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 T 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG T 5 C5 - N7 - C8 ANGL. DEV. = 3.7 DEGREES REMARK 500 DG T 5 N7 - C8 - N9 ANGL. DEV. = -3.5 DEGREES REMARK 500 DT T 6 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 DC T 7 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DA T 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DC T 9 O4' - C1' - C2' ANGL. DEV. = 3.9 DEGREES REMARK 500 DC T 9 N3 - C4 - C5 ANGL. DEV. = -2.6 DEGREES REMARK 500 DC T 9 N1 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DC T 9 C2 - N1 - C1' ANGL. DEV. = -6.7 DEGREES REMARK 500 DA T 10 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA T 10 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DC T 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC T 11 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC T 11 N3 - C2 - O2 ANGL. DEV. = -6.5 DEGREES REMARK 500 DT T 12 O4' - C1' - C2' ANGL. DEV. = 4.0 DEGREES REMARK 500 DT T 12 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT T 12 C5 - C4 - O4 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT P 1 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT P 1 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT P 1 C5 - C4 - O4 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA P 2 C5 - C6 - N1 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA P 2 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT P 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT P 4 N1 - C2 - O2 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG P 5 N3 - C4 - N9 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG P 7 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DG P 7 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG P 7 N9 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG P 7 N3 - C4 - N9 ANGL. DEV. = -5.2 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 39 67.04 64.00 REMARK 500 SER A 257 -7.81 85.91 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 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD1 REMARK 620 2 MET A 14 O 76.2 REMARK 620 3 ASP A 115 OD1 91.7 79.7 REMARK 620 4 0KX A 503 O2B 163.0 97.4 102.8 REMARK 620 5 0KX A 503 O2G 79.5 95.5 170.9 85.5 REMARK 620 6 0KX A 503 O1A 104.6 176.8 97.1 82.7 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 13 OD2 REMARK 620 2 ASP A 115 OD2 86.4 REMARK 620 3 GLU A 116 OE2 79.2 95.0 REMARK 620 4 0KX A 503 O1A 100.2 90.0 174.9 REMARK 620 5 DC P 9 O3' 155.1 86.0 77.9 103.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT T 101 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 4 N7 REMARK 620 2 CPT T 101 N1 86.5 REMARK 620 3 CPT T 101 N2 174.8 90.2 REMARK 620 4 DG T 5 N7 96.7 176.7 86.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CPT T 101 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG T 4 N7 REMARK 620 2 CPT T 101 N1 88.6 REMARK 620 3 CPT T 101 N2 177.1 89.9 REMARK 620 4 DG T 5 N7 95.1 175.8 86.4 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 MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0KX A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT T 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MR2 RELATED DB: PDB REMARK 900 RELATED ID: 3MR3 RELATED DB: PDB REMARK 900 RELATED ID: 3MR5 RELATED DB: PDB REMARK 900 RELATED ID: 3MR6 RELATED DB: PDB REMARK 900 RELATED ID: 3SI8 RELATED DB: PDB REMARK 900 RELATED ID: 4DL2 RELATED DB: PDB REMARK 900 RELATED ID: 4DL3 RELATED DB: PDB REMARK 900 RELATED ID: 4DL4 RELATED DB: PDB REMARK 900 RELATED ID: 4DL6 RELATED DB: PDB REMARK 900 RELATED ID: 4DL7 RELATED DB: PDB DBREF 4DL5 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432 DBREF 4DL5 T 1 12 PDB 4DL5 4DL5 1 12 DBREF 4DL5 P 1 9 PDB 4DL5 4DL5 1 9 SEQADV 4DL5 GLY A -2 UNP Q9Y253 EXPRESSION TAG SEQADV 4DL5 PRO A -1 UNP Q9Y253 EXPRESSION TAG SEQADV 4DL5 HIS A 0 UNP Q9Y253 EXPRESSION TAG SEQRES 1 A 435 GLY PRO HIS MET ALA THR GLY GLN ASP ARG VAL VAL ALA SEQRES 2 A 435 LEU VAL ASP MET ASP CYS PHE PHE VAL GLN VAL GLU GLN SEQRES 3 A 435 ARG GLN ASN PRO HIS LEU ARG ASN LYS PRO CYS ALA VAL SEQRES 4 A 435 VAL GLN TYR LYS SER TRP LYS GLY GLY GLY ILE ILE ALA SEQRES 5 A 435 VAL SER TYR GLU ALA ARG ALA PHE GLY VAL THR ARG SER SEQRES 6 A 435 MET TRP ALA ASP ASP ALA LYS LYS LEU CYS PRO ASP LEU SEQRES 7 A 435 LEU LEU ALA GLN VAL ARG GLU SER ARG GLY LYS ALA ASN SEQRES 8 A 435 LEU THR LYS TYR ARG GLU ALA SER VAL GLU VAL MET GLU SEQRES 9 A 435 ILE MET SER ARG PHE ALA VAL ILE GLU ARG ALA SER ILE SEQRES 10 A 435 ASP GLU ALA TYR VAL ASP LEU THR SER ALA VAL GLN GLU SEQRES 11 A 435 ARG LEU GLN LYS LEU GLN GLY GLN PRO ILE SER ALA ASP SEQRES 12 A 435 LEU LEU PRO SER THR TYR ILE GLU GLY LEU PRO GLN GLY SEQRES 13 A 435 PRO THR THR ALA GLU GLU THR VAL GLN LYS GLU GLY MET SEQRES 14 A 435 ARG LYS GLN GLY LEU PHE GLN TRP LEU ASP SER LEU GLN SEQRES 15 A 435 ILE ASP ASN LEU THR SER PRO ASP LEU GLN LEU THR VAL SEQRES 16 A 435 GLY ALA VAL ILE VAL GLU GLU MET ARG ALA ALA ILE GLU SEQRES 17 A 435 ARG GLU THR GLY PHE GLN CYS SER ALA GLY ILE SER HIS SEQRES 18 A 435 ASN LYS VAL LEU ALA LYS LEU ALA CYS GLY LEU ASN LYS SEQRES 19 A 435 PRO ASN ARG GLN THR LEU VAL SER HIS GLY SER VAL PRO SEQRES 20 A 435 GLN LEU PHE SER GLN MET PRO ILE ARG LYS ILE ARG SER SEQRES 21 A 435 LEU GLY GLY LYS LEU GLY ALA SER VAL ILE GLU ILE LEU SEQRES 22 A 435 GLY ILE GLU TYR MET GLY GLU LEU THR GLN PHE THR GLU SEQRES 23 A 435 SER GLN LEU GLN SER HIS PHE GLY GLU LYS ASN GLY SER SEQRES 24 A 435 TRP LEU TYR ALA MET CYS ARG GLY ILE GLU HIS ASP PRO SEQRES 25 A 435 VAL LYS PRO ARG GLN LEU PRO LYS THR ILE GLY CYS SER SEQRES 26 A 435 LYS ASN PHE PRO GLY LYS THR ALA LEU ALA THR ARG GLU SEQRES 27 A 435 GLN VAL GLN TRP TRP LEU LEU GLN LEU ALA GLN GLU LEU SEQRES 28 A 435 GLU GLU ARG LEU THR LYS ASP ARG ASN ASP ASN ASP ARG SEQRES 29 A 435 VAL ALA THR GLN LEU VAL VAL SER ILE ARG VAL GLN GLY SEQRES 30 A 435 ASP LYS ARG LEU SER SER LEU ARG ARG CYS CYS ALA LEU SEQRES 31 A 435 THR ARG TYR ASP ALA HIS LYS MET SER HIS ASP ALA PHE SEQRES 32 A 435 THR VAL ILE LYS ASN CYS ASN THR SER GLY ILE GLN THR SEQRES 33 A 435 GLU TRP SER PRO PRO LEU THR MET LEU PHE LEU CYS ALA SEQRES 34 A 435 THR LYS PHE SER ALA SER SEQRES 1 T 12 DT DA DC DG DG DT DC DA DC DA DC DT SEQRES 1 P 9 DT DA DG DT DG DT DG DA DC HET MG A 501 1 HET MG A 502 1 HET 0KX A 503 28 HET CPT T 101 6 HETNAM MG MAGNESIUM ION HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE HETNAM CPT CISPLATIN HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 4 MG 2(MG 2+) FORMUL 6 0KX C9 H17 N4 O12 P3 FORMUL 7 CPT CL2 H6 N2 PT HELIX 1 1 CYS A 16 ASN A 26 1 11 HELIX 2 2 PRO A 27 ARG A 30 5 4 HELIX 3 3 SER A 51 ALA A 56 1 6 HELIX 4 4 TRP A 64 CYS A 72 1 9 HELIX 5 5 LEU A 89 ALA A 107 1 19 HELIX 6 6 LEU A 121 LEU A 132 1 12 HELIX 7 7 SER A 138 LEU A 142 5 5 HELIX 8 8 GLU A 158 VAL A 161 5 4 HELIX 9 9 GLN A 162 LEU A 178 1 17 HELIX 10 10 SER A 185 GLY A 209 1 25 HELIX 11 11 ASN A 219 ASN A 230 1 12 HELIX 12 12 SER A 242 GLN A 249 1 8 HELIX 13 13 MET A 250 ILE A 255 5 6 HELIX 14 14 GLY A 260 GLY A 271 1 12 HELIX 15 15 TYR A 274 PHE A 281 5 8 HELIX 16 16 THR A 282 CYS A 302 1 21 HELIX 17 17 PRO A 326 ALA A 330 5 5 HELIX 18 18 ARG A 334 ASP A 360 1 27 HELIX 19 19 ASP A 391 LYS A 404 1 14 HELIX 20 20 ASN A 405 ASN A 407 5 3 SHEET 1 A 6 VAL A 108 SER A 113 0 SHEET 2 A 6 GLU A 116 ASP A 120 -1 O TYR A 118 N GLU A 110 SHEET 3 A 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119 SHEET 4 A 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9 SHEET 5 A 6 GLN A 235 LEU A 237 1 O THR A 236 N ALA A 214 SHEET 6 A 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237 SHEET 1 B 3 GLY A 46 VAL A 50 0 SHEET 2 B 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48 SHEET 3 B 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37 SHEET 1 C 2 ARG A 81 SER A 83 0 SHEET 2 C 2 LYS A 86 ASN A 88 -1 O ASN A 88 N ARG A 81 SHEET 1 D 3 ILE A 319 ASN A 324 0 SHEET 2 D 3 GLU A 414 ALA A 431 -1 O LEU A 424 N CYS A 321 SHEET 3 D 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415 SHEET 1 E 4 ILE A 319 ASN A 324 0 SHEET 2 E 4 GLU A 414 ALA A 431 -1 O LEU A 424 N CYS A 321 SHEET 3 E 4 ARG A 361 VAL A 372 -1 N VAL A 367 O CYS A 425 SHEET 4 E 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368 LINK OD1 ASP A 13 MG A MG A 501 1555 1555 2.41 LINK OD2 ASP A 13 MG A MG A 502 1555 1555 2.32 LINK O MET A 14 MG A MG A 501 1555 1555 2.29 LINK OD1 ASP A 115 MG A MG A 501 1555 1555 2.18 LINK OD2 ASP A 115 MG A MG A 502 1555 1555 2.21 LINK OE2 GLU A 116 MG A MG A 502 1555 1555 2.15 LINK MG A MG A 501 O2BA0KX A 503 1555 1555 2.14 LINK MG A MG A 501 O2GA0KX A 503 1555 1555 2.21 LINK MG A MG A 501 O1AA0KX A 503 1555 1555 2.28 LINK MG A MG A 502 O1AA0KX A 503 1555 1555 2.26 LINK MG A MG A 502 O3'A DC P 9 1555 1555 2.54 LINK N7 B DG T 4 PT1 BCPT T 101 1555 1555 2.06 LINK N7 A DG T 4 PT1 ACPT T 101 1555 1555 2.10 LINK N7 B DG T 5 PT1 BCPT T 101 1555 1555 2.10 LINK N7 A DG T 5 PT1 ACPT T 101 1555 1555 2.11 CISPEP 1 LEU A 150 PRO A 151 0 3.39 CISPEP 2 LYS A 231 PRO A 232 0 -1.14 CISPEP 3 SER A 416 PRO A 417 0 -7.54 SITE 1 AC1 6 ASP A 13 MET A 14 ASP A 115 MG A 502 SITE 2 AC1 6 0KX A 503 DC P 9 SITE 1 AC2 8 ASP A 13 SER A 113 ASP A 115 GLU A 116 SITE 2 AC2 8 MG A 501 0KX A 503 DA P 8 DC P 9 SITE 1 AC3 19 ASP A 13 MET A 14 ASP A 15 CYS A 16 SITE 2 AC3 19 PHE A 17 PHE A 18 ILE A 48 ALA A 49 SITE 3 AC3 19 TYR A 52 ARG A 55 ARG A 61 ASP A 115 SITE 4 AC3 19 LYS A 231 MG A 501 MG A 502 DA P 8 SITE 5 AC3 19 DC P 9 DG T 4 DG T 5 SITE 1 AC4 5 DA P 8 DG T 4 DG T 5 DT T 6 SITE 2 AC4 5 DC T 7 CRYST1 99.414 99.414 82.085 90.00 90.00 120.00 P 61 6 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 0.010059 0.005808 0.000000 0.00000 SCALE2 0.000000 0.011615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012182 0.00000