HEADER TRANSFERASE/DNA 16-FEB-13 4J9K
TITLE HUMAN DNA POLYMERASE ETA-DNA TERNARY COMPLEX: MISINCORPORATION G
TITLE 2 OPPOSITE T AFTER A T AT THE PRIMER 3' END (TA/G)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE ETA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC CORE DOMAIN, 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;
COMPND 10 CHAIN: T;
COMPND 11 ENGINEERED: YES;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: DNA;
COMPND 14 CHAIN: P;
COMPND 15 ENGINEERED: YES
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 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 IMMUNOGLOBULIN, A TO G TRANSITION, MISINCORPORATION, WOBBLE BASE
KEYWDS 2 PAIR, DNA POLYMERASE, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.ZHAO,M.GREGORY,C.BIERTUMPFEL,Y.HUA,F.HANAOKA,W.YANG
REVDAT 3 20-SEP-23 4J9K 1 REMARK SEQADV LINK
REVDAT 2 28-AUG-13 4J9K 1 JRNL
REVDAT 1 01-MAY-13 4J9K 0
JRNL AUTH Y.ZHAO,M.T.GREGORY,C.BIERTUMPFEL,Y.J.HUA,F.HANAOKA,W.YANG
JRNL TITL MECHANISM OF SOMATIC HYPERMUTATION AT THE WA MOTIF BY HUMAN
JRNL TITL 2 DNA POLYMERASE ETA.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 8146 2013
JRNL REFN ISSN 0027-8424
JRNL PMID 23630267
JRNL DOI 10.1073/PNAS.1303126110
REMARK 2
REMARK 2 RESOLUTION. 2.03 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.8_1069
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) : 2.03
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.87
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2
REMARK 3 NUMBER OF REFLECTIONS : 28363
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) : 0.164
REMARK 3 FREE R VALUE : 0.187
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.620
REMARK 3 FREE R VALUE TEST SET COUNT : 2161
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 26.8764 - 4.9817 0.90 1675 137 0.1914 0.2112
REMARK 3 2 4.9817 - 3.9582 0.94 1728 134 0.1418 0.1406
REMARK 3 3 3.9582 - 3.4590 0.95 1729 153 0.1372 0.1604
REMARK 3 4 3.4590 - 3.1433 0.96 1747 138 0.1464 0.1651
REMARK 3 5 3.1433 - 2.9183 0.96 1745 138 0.1632 0.1805
REMARK 3 6 2.9183 - 2.7464 0.95 1744 129 0.1605 0.1809
REMARK 3 7 2.7464 - 2.6090 0.96 1744 144 0.1664 0.1993
REMARK 3 8 2.6090 - 2.4955 0.97 1755 150 0.1725 0.2158
REMARK 3 9 2.4955 - 2.3995 0.97 1693 182 0.1769 0.2144
REMARK 3 10 2.3995 - 2.3167 0.98 1793 135 0.1673 0.2206
REMARK 3 11 2.3167 - 2.2443 0.98 1769 129 0.1800 0.2223
REMARK 3 12 2.2443 - 2.1802 0.98 1788 151 0.1835 0.2072
REMARK 3 13 2.1802 - 2.1228 0.98 1756 162 0.1826 0.2411
REMARK 3 14 2.1228 - 2.0711 0.98 1781 120 0.1935 0.2174
REMARK 3 15 2.0711 - 2.0300 0.97 1755 159 0.1833 0.1824
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) : 0.150
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.550
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 23.07
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.69
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 : 0.006 4118
REMARK 3 ANGLE : 0.981 5665
REMARK 3 CHIRALITY : 0.057 631
REMARK 3 PLANARITY : 0.004 656
REMARK 3 DIHEDRAL : 20.310 1606
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 4J9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-13.
REMARK 100 THE DEPOSITION ID IS D_1000077767.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-JAN-10
REMARK 200 TEMPERATURE (KELVIN) : 95
REMARK 200 PH : 6.5
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 : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28419
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 4.500
REMARK 200 R MERGE (I) : 0.10200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9
REMARK 200 DATA REDUNDANCY IN SHELL : 3.90
REMARK 200 R MERGE FOR SHELL (I) : 0.61500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.050
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 3MR2
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 40.64
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG2K-MME, KCL, MES, PH 6.5, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K
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 27.22500
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 54.45000
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 40.83750
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 68.06250
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 13.61250
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: 6070 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21710 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 155
REMARK 465 THR A 156
REMARK 465 ALA A 157
REMARK 465 GLU A 158
REMARK 465 GLU A 159
REMARK 465 DT T 1
REMARK 465 DC T 2
REMARK 465 DT P 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 DA T 3 P OP1 OP2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 SER A 177 O - C - N ANGL. DEV. = -13.6 DEGREES
REMARK 500 DA P 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DT P 9 O4' - C1' - N1 ANGL. DEV. = 3.7 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 CYS A 16 58.24 25.91
REMARK 500 TYR A 39 177.74 73.50
REMARK 500 LYS A 40 -40.31 -144.29
REMARK 500 SER A 62 -2.74 83.15
REMARK 500 ASP A 181 4.85 107.94
REMARK 500 SER A 185 131.71 -34.67
REMARK 500 SER A 217 -159.94 -159.12
REMARK 500 SER A 257 -6.24 93.51
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 XG4 A 506
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 75.8
REMARK 620 3 ASP A 115 OD1 95.3 80.7
REMARK 620 4 XG4 A 503 O1A 108.8 168.7 88.5
REMARK 620 5 XG4 A 503 O1B 162.2 87.8 88.6 88.6
REMARK 620 6 XG4 A 503 O1G 77.6 88.8 168.6 102.1 95.6
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 83.5
REMARK 620 3 GLU A 116 OE2 84.6 95.6
REMARK 620 4 XG4 A 503 O1A 99.1 88.1 175.1
REMARK 620 5 HOH A 744 O 94.4 173.6 90.2 86.4
REMARK 620 6 HOH A 828 O 161.7 91.6 78.3 98.4 92.2
REMARK 620 7 DT P 9 O3' 174.0 96.4 89.5 86.9 86.4 12.6
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 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 XG4 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 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XG4 A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL P 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL P 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL P 103
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3MR2 RELATED DB: PDB
REMARK 900 RELATED ID: 4DL2 RELATED DB: PDB
REMARK 900 RELATED ID: 4DL3 RELATED DB: PDB
REMARK 900 RELATED ID: 4J9L RELATED DB: PDB
REMARK 900 RELATED ID: 4J9M RELATED DB: PDB
REMARK 900 RELATED ID: 4J9N RELATED DB: PDB
REMARK 900 RELATED ID: 4J9O RELATED DB: PDB
REMARK 900 RELATED ID: 4J9P RELATED DB: PDB
REMARK 900 RELATED ID: 4J9Q RELATED DB: PDB
REMARK 900 RELATED ID: 4J9R RELATED DB: PDB
REMARK 900 RELATED ID: 4J9S RELATED DB: PDB
DBREF 4J9K A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 4J9K T 1 13 PDB 4J9K 4J9K 1 13
DBREF 4J9K P 1 9 PDB 4J9K 4J9K 1 9
SEQADV 4J9K GLY A -2 UNP Q9Y253 EXPRESSION TAG
SEQADV 4J9K PRO A -1 UNP Q9Y253 EXPRESSION TAG
SEQADV 4J9K 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 13 DT DC DA DT DT DA DT DG DA DC DG DC DT
SEQRES 1 P 9 DT DA DG DC DG DT DC DA DT
HET MG A 501 1
HET MG A 502 1
HET XG4 A 503 31
HET GOL A 504 6
HET GOL A 505 6
HET XG4 A 506 12
HET GOL T 101 6
HET GOL P 101 6
HET GOL P 102 6
HET GOL P 103 6
HETNAM MG MAGNESIUM ION
HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 4 MG 2(MG 2+)
FORMUL 6 XG4 2(C10 H17 N6 O12 P3)
FORMUL 7 GOL 6(C3 H8 O3)
FORMUL 14 HOH *261(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 GLN A 133 1 13
HELIX 7 7 SER A 138 LEU A 142 5 5
HELIX 8 8 GLN A 162 ASP A 181 1 20
HELIX 9 9 THR A 184 GLY A 209 1 26
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 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 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 ARG A 81 SER A 83 0
SHEET 2 C 2 LYS A 86 ASN A 88 -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 OD1 ASP A 13 MG MG A 501 1555 1555 2.12
LINK OD2 ASP A 13 MG MG A 502 1555 1555 2.03
LINK O MET A 14 MG MG A 501 1555 1555 2.35
LINK OD1 ASP A 115 MG MG A 501 1555 1555 2.21
LINK OD2 ASP A 115 MG MG A 502 1555 1555 2.27
LINK OE2 GLU A 116 MG MG A 502 1555 1555 2.18
LINK MG MG A 501 O1A XG4 A 503 1555 1555 2.00
LINK MG MG A 501 O1B XG4 A 503 1555 1555 2.04
LINK MG MG A 501 O1G XG4 A 503 1555 1555 2.06
LINK MG MG A 502 O1A XG4 A 503 1555 1555 2.20
LINK MG MG A 502 O HOH A 744 1555 1555 2.19
LINK MG MG A 502 O AHOH A 828 1555 1555 2.47
LINK MG MG A 502 O3'B DT P 9 1555 1555 2.70
CISPEP 1 LEU A 150 PRO A 151 0 1.94
CISPEP 2 LYS A 231 PRO A 232 0 1.49
CISPEP 3 SER A 416 PRO A 417 0 -0.39
SITE 1 AC1 5 ASP A 13 MET A 14 ASP A 115 MG A 502
SITE 2 AC1 5 XG4 A 503
SITE 1 AC2 8 ASP A 13 ASP A 115 GLU A 116 MG A 501
SITE 2 AC2 8 XG4 A 503 HOH A 744 HOH A 828 DT P 9
SITE 1 AC3 28 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC3 28 PHE A 17 PHE A 18 GLN A 38 ILE A 48
SITE 3 AC3 28 ALA A 49 TYR A 52 ARG A 55 ARG A 61
SITE 4 AC3 28 ASP A 115 LYS A 231 MG A 501 MG A 502
SITE 5 AC3 28 HOH A 614 HOH A 641 HOH A 643 HOH A 699
SITE 6 AC3 28 HOH A 713 HOH A 734 HOH A 744 HOH A 788
SITE 7 AC3 28 HOH A 828 DT P 9 DT T 5 DA T 6
SITE 1 AC4 11 ARG A 24 GLN A 25 PRO A 244 PHE A 247
SITE 2 AC4 11 SER A 248 GLY A 276 GLU A 277 HOH A 630
SITE 3 AC4 11 HOH A 656 HOH A 752 HOH A 776
SITE 1 AC5 8 GLU A 148 GLY A 149 LEU A 150 MET A 166
SITE 2 AC5 8 THR A 388 ARG A 389 HOH A 657 HOH A 675
SITE 1 AC6 4 SER A 257 LYS A 293 ASN A 294 TRP A 297
SITE 1 AC7 7 THR A 318 PHE A 423 CYS A 425 DG T 8
SITE 2 AC7 7 DA T 9 DC T 10 HOH T 207
SITE 1 AC8 3 CYS A 384 DG P 3 DC P 4
SITE 1 AC9 5 DC P 7 DA P 8 DG T 8 DA T 9
SITE 2 AC9 5 DC T 10
SITE 1 BC1 8 PHE A 325 THR A 329 LEU A 331 GLN A 336
SITE 2 BC1 8 TRP A 340 DG P 3 DC P 4 DT T 13
CRYST1 98.584 98.584 81.675 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 0.010144 0.005856 0.000000 0.00000
SCALE2 0.000000 0.011713 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012244 0.00000