HEADER TRANSFERASE/DNA 18-DEC-13 4O3P
TITLE CRYSTAL STRUCTURE OF HUMAN POLYMERASE ETA INSERTING DCTP OPPOSITE AN
TITLE 2 8-OXOG CONTAINING DNA TEMPLATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE ETA;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: RAD30 HOMOLOG A, XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN;
COMPND 5 EC: 2.7.7.7;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: DNA (5'-D(*CP*AP*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3');
COMPND 9 CHAIN: T;
COMPND 10 ENGINEERED: YES;
COMPND 11 OTHER_DETAILS: NUCLEIC ACIDS TEMPLATE: CAT (8OG)AT GAC GCT;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3');
COMPND 14 CHAIN: P;
COMPND 15 ENGINEERED: YES;
COMPND 16 OTHER_DETAILS: NUCLEIC ACIDS PRIMAR: AGCGTCAT
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: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 11 MOL_ID: 3;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS CATALYTIC DOMAIN, DNA, DNA DAMAGE, DNA-DIRECTED DNA POLYMERASE,
KEYWDS 2 CYTOSINE TRIPHOSPHATE, Y-FAMILY POLYMERASE, TRANS-LESION SYNTHESIS
KEYWDS 3 (TLS), DNA BINDING, 8-OXOG LESION BYPASS, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PATRA,M.EGLI
REVDAT 3 20-SEP-23 4O3P 1 REMARK SEQADV LINK
REVDAT 2 02-JUL-14 4O3P 1 JRNL
REVDAT 1 30-APR-14 4O3P 0
JRNL AUTH A.PATRA,L.D.NAGY,Q.ZHANG,Y.SU,L.MULLER,F.P.GUENGERICH,M.EGLI
JRNL TITL KINETICS, STRUCTURE, AND MECHANISM OF
JRNL TITL 2 8-OXO-7,8-DIHYDRO-2'-DEOXYGUANOSINE BYPASS BY HUMAN DNA
JRNL TITL 3 POLYMERASE ETA
JRNL REF J.BIOL.CHEM. V. 289 16867 2014
JRNL REFN ISSN 0021-9258
JRNL PMID 24759104
JRNL DOI 10.1074/JBC.M114.551820
REMARK 2
REMARK 2 RESOLUTION. 1.72 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1551)
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) : 1.72
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.52
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 47409
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.165
REMARK 3 R VALUE (WORKING SET) : 0.163
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060
REMARK 3 FREE R VALUE TEST SET COUNT : 2400
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 42.5340 - 4.4215 1.00 2682 165 0.1699 0.1962
REMARK 3 2 4.4215 - 3.5100 1.00 2657 153 0.1386 0.1709
REMARK 3 3 3.5100 - 3.0665 1.00 2674 131 0.1450 0.1758
REMARK 3 4 3.0665 - 2.7862 1.00 2646 158 0.1678 0.2382
REMARK 3 5 2.7862 - 2.5865 1.00 2645 133 0.1685 0.2200
REMARK 3 6 2.5865 - 2.4340 1.00 2654 157 0.1808 0.2432
REMARK 3 7 2.4340 - 2.3121 1.00 2659 127 0.1670 0.2259
REMARK 3 8 2.3121 - 2.2115 1.00 2657 125 0.1643 0.2425
REMARK 3 9 2.2115 - 2.1264 1.00 2634 114 0.1570 0.2003
REMARK 3 10 2.1264 - 2.0530 1.00 2651 141 0.1537 0.1884
REMARK 3 11 2.0530 - 1.9888 1.00 2651 141 0.1604 0.2112
REMARK 3 12 1.9888 - 1.9319 1.00 2628 146 0.1623 0.2218
REMARK 3 13 1.9319 - 1.8811 1.00 2622 153 0.1772 0.2345
REMARK 3 14 1.8811 - 1.8352 1.00 2681 129 0.1768 0.2455
REMARK 3 15 1.8352 - 1.7935 1.00 2590 133 0.1874 0.2500
REMARK 3 16 1.7935 - 1.7553 1.00 2632 156 0.1981 0.2448
REMARK 3 17 1.7553 - 1.7202 1.00 2646 138 0.2156 0.2702
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.440
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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 : 0.011 4039
REMARK 3 ANGLE : 1.387 5553
REMARK 3 CHIRALITY : 0.059 616
REMARK 3 PLANARITY : 0.006 643
REMARK 3 DIHEDRAL : 19.363 1600
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 4O3P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-14.
REMARK 100 THE DEPOSITION ID IS D_1000084002.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-JUL-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49366
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 7.300
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : 0.07000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.5680
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 6.70
REMARK 200 R MERGE FOR SHELL (I) : 0.69800
REMARK 200 R SYM FOR SHELL (I) : 0.69800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.730
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER (MR)
REMARK 200 STARTING MODEL: PDB ENTRY 4ECQ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 5.5, 5MM MAGNESIUM
REMARK 280 CHLORIDE, 16% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 291.0K
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 27.18367
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 54.36733
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 40.77550
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 67.95917
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 13.59183
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: 5780 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21910 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 THR A 156
REMARK 465 ALA A 157
REMARK 465 GLU A 158
REMARK 465 GLU A 159
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 1 O5' C5' C4' O4' C3' C2' C1'
REMARK 470 DC T 1 N1 C2 O2 N3 C4 N4 C5
REMARK 470 DC T 1 C6
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 O HOH A 717 O HOH A 935 1.94
REMARK 500 NH2 ARG A 256 O HOH A 626 1.95
REMARK 500 O HOH A 699 O HOH A 852 1.99
REMARK 500 O HOH A 906 O HOH P 118 2.01
REMARK 500 O HOH A 920 O HOH A 946 2.05
REMARK 500 O HOH A 855 O HOH A 900 2.07
REMARK 500 O HOH A 755 O HOH A 882 2.09
REMARK 500 O HOH A 863 O HOH A 864 2.09
REMARK 500 OE1 GLU A 94 O HOH A 924 2.10
REMARK 500 O HOH A 963 O HOH A 964 2.11
REMARK 500 O HOH A 683 O HOH A 953 2.12
REMARK 500 O HOH A 859 O HOH A 905 2.13
REMARK 500 O HOH A 769 O HOH A 891 2.13
REMARK 500 OD2 ASP A 308 O HOH A 947 2.14
REMARK 500 O HOH A 840 O HOH A 931 2.14
REMARK 500 NH2 ARG A 206 O HOH A 899 2.15
REMARK 500 O HOH A 700 O HOH A 852 2.15
REMARK 500 O HOH A 679 O HOH A 930 2.15
REMARK 500 O HOH A 689 O HOH A 886 2.15
REMARK 500 O HOH A 613 O HOH A 857 2.16
REMARK 500 O HOH A 990 O HOH A 997 2.16
REMARK 500 NH2 ARG A 313 O HOH A 901 2.16
REMARK 500 NE2 GLN A 179 O HOH A 993 2.16
REMARK 500 O2 DT T 3 O HOH T 129 2.19
REMARK 500 OD2 ASP A 74 O HOH A 889 2.19
REMARK 500 O HOH A 803 O HOH A 965 2.19
REMARK 500 O HOH A 883 O HOH A 968 2.19
REMARK 500 OE1 GLU A 101 O HOH A 882 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 6 O3' DT T 6 C3' -0.045
REMARK 500 DG T 7 O3' DG T 7 C3' -0.039
REMARK 500 DC T 9 O3' DC T 9 C3' -0.047
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 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DC T 9 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES
REMARK 500 DG P 2 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DA P 7 O4' - C4' - C3' ANGL. DEV. = -3.1 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 CYS A 16 63.18 23.40
REMARK 500 TYR A 39 80.51 68.54
REMARK 500 SER A 62 -12.63 77.42
REMARK 500 SER A 217 -158.26 -152.03
REMARK 500 SER A 257 -12.71 92.11
REMARK 500 LYS A 376 -12.48 -155.68
REMARK 500 ASN A 407 94.53 -66.88
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 502 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD2
REMARK 620 2 MET A 14 O 83.3
REMARK 620 3 ASP A 115 OD2 96.2 86.8
REMARK 620 4 0KX A 501 O1G 86.4 96.0 176.4
REMARK 620 5 0KX A 501 O1B 169.1 89.8 91.8 86.0
REMARK 620 6 0KX A 501 O2A 101.5 170.5 84.5 92.6 86.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 ASP A 115 OD1 97.5
REMARK 620 3 GLU A 116 OE1 87.6 95.5
REMARK 620 4 0KX A 501 O2A 99.3 88.9 171.3
REMARK 620 5 HOH A 601 O 85.7 168.8 95.4 80.0
REMARK 620 6 DT P 8 O3' 165.6 93.4 82.0 90.3 85.5
REMARK 620 7 DT P 8 O3' 166.9 86.5 79.5 93.3 92.9 7.7
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 0KX 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 MG A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4O3N RELATED DB: PDB
REMARK 900 RELATED ID: 4O3O RELATED DB: PDB
REMARK 900 RELATED ID: 4O3Q RELATED DB: PDB
REMARK 900 RELATED ID: 4O3R RELATED DB: PDB
REMARK 900 RELATED ID: 4O3S RELATED DB: PDB
DBREF 4O3P A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 4O3P T 1 12 PDB 4O3P 4O3P 1 12
DBREF 4O3P P 1 8 PDB 4O3P 4O3P 1 8
SEQADV 4O3P GLY A -2 UNP Q9Y253 EXPRESSION TAG
SEQADV 4O3P PRO A -1 UNP Q9Y253 EXPRESSION TAG
SEQADV 4O3P 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 DC DA DT 8OG DA DT DG DA DC DG DC DT
SEQRES 1 P 8 DA DG DC DG DT DC DA DT
MODRES 4O3P 8OG T 4 DG
HET 8OG T 4 23
HET 0KX A 501 28
HET MG A 502 1
HET MG A 503 1
HET GOL A 504 6
HET GOL A 505 6
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETNAM 0KX 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 0KX PHOSPHORYL]AMINO}PHOSPHORYL]CYTIDINE
HETNAM MG MAGNESIUM ION
HETNAM GOL GLYCEROL
HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 8OG C10 H14 N5 O8 P
FORMUL 4 0KX C9 H17 N4 O12 P3
FORMUL 5 MG 2(MG 2+)
FORMUL 7 GOL 2(C3 H8 O3)
FORMUL 9 HOH *466(H2 O)
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 GLN A 162 LEU A 178 1 17
HELIX 9 9 SER A 185 GLY A 209 1 25
HELIX 10 10 ASN A 219 ASN A 230 1 12
HELIX 11 11 SER A 242 GLN A 249 1 8
HELIX 12 12 MET A 250 ILE A 255 5 6
HELIX 13 13 GLY A 260 GLY A 271 1 12
HELIX 14 14 TYR A 274 PHE A 281 5 8
HELIX 15 15 THR A 282 GLY A 291 1 10
HELIX 16 16 GLY A 291 CYS A 302 1 12
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 ILE A 109 SER A 113 0
SHEET 2 A 6 GLU A 116 ASP A 120 -1 O GLU A 116 N ALA A 112
SHEET 3 A 6 VAL A 9 MET A 14 -1 N VAL A 12 O ALA A 117
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 ILE A 216
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 GLU A 82 SER A 83 0
SHEET 2 C 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83
SHEET 1 D 3 ILE A 319 ASN A 324 0
SHEET 2 D 3 GLU A 414 ALA A 431 -1 O ALA A 426 N ILE A 319
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 ALA A 426 N ILE A 319
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 O3' DT T 3 P 8OG T 4 1555 1555 1.61
LINK O3' 8OG T 4 P DA T 5 1555 1555 1.61
LINK OD2 ASP A 13 MG MG A 502 1555 1555 2.04
LINK OD1 ASP A 13 MG MG A 503 1555 1555 2.06
LINK O MET A 14 MG MG A 502 1555 1555 2.13
LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.12
LINK OD1 ASP A 115 MG MG A 503 1555 1555 2.07
LINK OE1 GLU A 116 MG MG A 503 1555 1555 2.08
LINK O1G 0KX A 501 MG MG A 502 1555 1555 2.08
LINK O1B 0KX A 501 MG MG A 502 1555 1555 2.09
LINK O2A 0KX A 501 MG MG A 502 1555 1555 2.21
LINK O2A 0KX A 501 MG MG A 503 1555 1555 2.18
LINK MG MG A 503 O HOH A 601 1555 1555 2.18
LINK MG MG A 503 O3'B DT P 8 1555 1555 2.19
LINK MG MG A 503 O3'A DT P 8 1555 1555 2.33
CISPEP 1 LEU A 150 PRO A 151 0 2.29
CISPEP 2 LYS A 231 PRO A 232 0 0.86
CISPEP 3 SER A 416 PRO A 417 0 -4.86
SITE 1 AC1 26 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC1 26 PHE A 17 PHE A 18 ILE A 48 ALA A 49
SITE 3 AC1 26 TYR A 52 ARG A 55 ARG A 61 ASP A 115
SITE 4 AC1 26 LYS A 231 MG A 502 MG A 503 HOH A 601
SITE 5 AC1 26 HOH A 602 HOH A 603 HOH A 604 HOH A 607
SITE 6 AC1 26 HOH A 669 HOH A 670 HOH A 893 DT P 8
SITE 7 AC1 26 HOH P 102 8OG T 4
SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 0KX A 501
SITE 2 AC2 5 MG A 503
SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 0KX A 501
SITE 2 AC3 7 MG A 502 HOH A 601 DT P 8
SITE 1 AC4 10 ARG A 24 PRO A 244 PHE A 247 SER A 248
SITE 2 AC4 10 GLY A 276 GLU A 277 HOH A 694 HOH A 695
SITE 3 AC4 10 HOH A 735 HOH A 818
SITE 1 AC5 5 GLN A 20 ARG A 30 GLY A 209 GLN A 245
SITE 2 AC5 5 HOH A 704
CRYST1 98.198 98.198 81.551 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 0.010184 0.005879 0.000000 0.00000
SCALE2 0.000000 0.011759 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012262 0.00000