HEADER REPLICATION, TRANSFERASE/DNA 12-JUN-16 5KFC
TITLE HUMAN DNA POLYMERASE ETA-DNA TERNARY COMPLEX: REACTION WITH 1 MM MN2+
TITLE 2 FOR 180S
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*TP*AP*TP*GP*AP*CP*GP*CP*T)-3');
COMPND 9 CHAIN: T;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3');
COMPND 13 CHAIN: P;
COMPND 14 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: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28;
SOURCE 11 MOL_ID: 2;
SOURCE 12 SYNTHETIC: YES;
SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 14 ORGANISM_TAXID: 9606;
SOURCE 15 MOL_ID: 3;
SOURCE 16 SYNTHETIC: YES;
SOURCE 17 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 18 ORGANISM_TAXID: 9606
KEYWDS IN CRYSTALLO REACTION, DNA POLYMERASE, METAL ION DEPENDENT CATALYSIS,
KEYWDS 2 REPLICATION, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.GAO,W.YANG
REVDAT 4 27-SEP-23 5KFC 1 LINK
REVDAT 3 25-DEC-19 5KFC 1 REMARK
REVDAT 2 20-SEP-17 5KFC 1 REMARK
REVDAT 1 22-JUN-16 5KFC 0
JRNL AUTH Y.GAO,W.YANG
JRNL TITL CAPTURE OF A THIRD MG2+ IS ESSENTIAL FOR CATALYZING DNA
JRNL TITL 2 SYNTHESIS.
JRNL REF SCIENCE V. 352 1334 2016
JRNL REFN ESSN 1095-9203
JRNL PMID 27284197
JRNL DOI 10.1126/SCIENCE.AAD9633
REMARK 2
REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 71649
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.180
REMARK 3 FREE R VALUE : 0.210
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.730
REMARK 3 FREE R VALUE TEST SET COUNT : 5535
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
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) : 20.360
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 23.02
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.97
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 : NULL NULL
REMARK 3 ANGLE : NULL NULL
REMARK 3 CHIRALITY : NULL NULL
REMARK 3 PLANARITY : NULL NULL
REMARK 3 DIHEDRAL : NULL NULL
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 5KFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-16.
REMARK 100 THE DEPOSITION ID IS D_1000222109.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 03-JUL-14
REMARK 200 TEMPERATURE (KELVIN) : 100
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-ID
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 CRYSTAL-LIQUID NITROGEN
REMARK 200 COOLED
REMARK 200 OPTICS : 4*4 MOSIAC
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71666
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 4.600
REMARK 200 R MERGE (I) : 0.04300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.5600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.41300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.510
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: 4ECQ
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.08
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 2000MME, 0.1 M MES, PH 6.0,
REMARK 280 EVAPORATION, 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 27.36333
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 54.72667
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 41.04500
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 68.40833
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 13.68167
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: 5720 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21970 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 OG SER A 409 O ILE A 411 2.18
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 PRO A 232 CD PRO A 232 N 0.088
REMARK 500 CYS A 321 CB CYS A 321 SG -0.236
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 LYS A 40 CA - C - O ANGL. DEV. = 16.8 DEGREES
REMARK 500 LYS A 40 CA - C - N ANGL. DEV. = -16.1 DEGREES
REMARK 500 CYS A 321 CA - CB - SG ANGL. DEV. = 23.7 DEGREES
REMARK 500 CYS A 321 CA - CB - SG ANGL. DEV. = 15.0 DEGREES
REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DA P 7 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES
REMARK 500 DA P 7 O4' - C1' - N9 ANGL. DEV. = 2.0 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 62.91 30.86
REMARK 500 TYR A 39 -174.08 68.96
REMARK 500 LYS A 40 -30.45 -159.12
REMARK 500 SER A 62 -10.42 79.87
REMARK 500 SER A 217 -157.48 -153.27
REMARK 500 SER A 257 -10.81 93.26
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 MN A 501 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD2
REMARK 620 2 ASP A 13 OD2 25.3
REMARK 620 3 ASP A 115 OD1 110.8 90.8
REMARK 620 4 GLU A 116 OE2 74.9 91.7 95.9
REMARK 620 5 DTP A 506 O1A 113.4 99.8 91.3 166.3
REMARK 620 6 HOH A 791 O 71.7 88.8 170.2 93.9 79.1
REMARK 620 7 DT P 8 O3' 153.0 176.2 88.4 84.7 83.8 92.6
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 502 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 MET A 14 O 96.0
REMARK 620 3 ASP A 115 OD2 86.9 85.9
REMARK 620 4 DTP A 506 O1B 172.0 89.3 87.4
REMARK 620 5 DTP A 506 O1A 89.7 168.8 84.7 84.1
REMARK 620 6 DTP A 506 O1G 102.0 101.6 167.5 82.9 86.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MN A 503 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 MET A 14 O 83.7
REMARK 620 3 ASP A 115 OD2 107.5 86.0
REMARK 620 4 DTP A 506 O1B 162.8 89.1 87.5
REMARK 620 5 DTP A 506 O1A 105.2 169.0 85.1 84.1
REMARK 620 6 DTP A 506 O1G 83.6 101.2 167.5 82.5 86.5
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN 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 DTP A 506
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5KFA RELATED DB: PDB
REMARK 900 RELATED ID: 5KFB RELATED DB: PDB
REMARK 900 RELATED ID: 5KG0 RELATED DB: PDB
REMARK 900 RELATED ID: 5KG1 RELATED DB: PDB
REMARK 900 RELATED ID: 5KG2 RELATED DB: PDB
REMARK 900 RELATED ID: 5KG3 RELATED DB: PDB
REMARK 900 RELATED ID: 5KG4 RELATED DB: PDB
REMARK 900 RELATED ID: 5KG5 RELATED DB: PDB
REMARK 900 RELATED ID: 5KG6 RELATED DB: PDB
REMARK 900 RELATED ID: 5KG7 RELATED DB: PDB
REMARK 900 RELATED ID: 5KFD RELATED DB: PDB
REMARK 900 RELATED ID: 5KFE RELATED DB: PDB
REMARK 900 RELATED ID: 5KFS RELATED DB: PDB
REMARK 900 RELATED ID: 5KFT RELATED DB: PDB
REMARK 900 RELATED ID: 5KFU RELATED DB: PDB
REMARK 900 RELATED ID: 5KFV RELATED DB: PDB
REMARK 900 RELATED ID: 5KFW RELATED DB: PDB
REMARK 900 RELATED ID: 5KFX RELATED DB: PDB
REMARK 900 RELATED ID: 5KFG RELATED DB: PDB
REMARK 900 RELATED ID: 5KFY RELATED DB: PDB
REMARK 900 RELATED ID: 5KFZ RELATED DB: PDB
REMARK 900 RELATED ID: 5KFH RELATED DB: PDB
REMARK 900 RELATED ID: 5KFK RELATED DB: PDB
REMARK 900 RELATED ID: 5KFL RELATED DB: PDB
REMARK 900 RELATED ID: 5KFI RELATED DB: PDB
REMARK 900 RELATED ID: 5KFJ RELATED DB: PDB
REMARK 900 RELATED ID: 5KFM RELATED DB: PDB
REMARK 900 RELATED ID: 5KFN RELATED DB: PDB
REMARK 900 RELATED ID: 5KFO RELATED DB: PDB
REMARK 900 RELATED ID: 5KFP RELATED DB: PDB
REMARK 900 RELATED ID: 5KFQ RELATED DB: PDB
REMARK 900 RELATED ID: 5KFR RELATED DB: PDB
REMARK 900 RELATED ID: 5KFF RELATED DB: PDB
DBREF 5KFC A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 5KFC T 1 12 PDB 5KFC 5KFC 1 12
DBREF 5KFC P 1 8 PDB 5KFC 5KFC 1 8
SEQADV 5KFC GLY A -2 UNP Q9Y253 EXPRESSION TAG
SEQADV 5KFC PRO A -1 UNP Q9Y253 EXPRESSION TAG
SEQADV 5KFC 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 DT DA DT DG DA DC DG DC DT
SEQRES 1 P 8 DA DG DC DG DT DC DA DT
HET MN A 501 1
HET CA A 502 1
HET MN A 503 1
HET GOL A 504 6
HET GOL A 505 6
HET DTP A 506 30
HETNAM MN MANGANESE (II) ION
HETNAM CA CALCIUM ION
HETNAM GOL GLYCEROL
HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 4 MN 2(MN 2+)
FORMUL 5 CA CA 2+
FORMUL 7 GOL 2(C3 H8 O3)
FORMUL 9 DTP C10 H16 N5 O12 P3
FORMUL 10 HOH *441(H2 O)
HELIX 1 AA1 CYS A 16 ASN A 26 1 11
HELIX 2 AA2 PRO A 27 ARG A 30 5 4
HELIX 3 AA3 SER A 51 ALA A 56 1 6
HELIX 4 AA4 TRP A 64 CYS A 72 1 9
HELIX 5 AA5 LEU A 89 SER A 104 1 16
HELIX 6 AA6 LEU A 121 GLN A 133 1 13
HELIX 7 AA7 SER A 138 LEU A 142 5 5
HELIX 8 AA8 GLN A 162 LEU A 178 1 17
HELIX 9 AA9 SER A 185 GLY A 209 1 25
HELIX 10 AB1 ASN A 219 ASN A 230 1 12
HELIX 11 AB2 SER A 242 GLN A 249 1 8
HELIX 12 AB3 MET A 250 ILE A 255 5 6
HELIX 13 AB4 GLY A 260 GLY A 271 1 12
HELIX 14 AB5 TYR A 274 PHE A 281 5 8
HELIX 15 AB6 THR A 282 GLY A 291 1 10
HELIX 16 AB7 GLY A 291 CYS A 302 1 12
HELIX 17 AB8 PRO A 326 ALA A 330 5 5
HELIX 18 AB9 ARG A 334 ASP A 360 1 27
HELIX 19 AC1 ASP A 391 LYS A 404 1 14
HELIX 20 AC2 ASN A 405 ASN A 407 5 3
SHEET 1 AA1 6 ILE A 109 SER A 113 0
SHEET 2 AA1 6 GLU A 116 ASP A 120 -1 O GLU A 116 N ALA A 112
SHEET 3 AA1 6 VAL A 9 MET A 14 -1 N ALA A 10 O VAL A 119
SHEET 4 AA1 6 CYS A 212 SER A 217 -1 O SER A 217 N VAL A 9
SHEET 5 AA1 6 GLN A 235 LEU A 237 1 O THR A 236 N ILE A 216
SHEET 6 AA1 6 THR A 145 ILE A 147 1 N TYR A 146 O LEU A 237
SHEET 1 AA2 3 GLY A 46 VAL A 50 0
SHEET 2 AA2 3 CYS A 34 GLN A 38 -1 N VAL A 36 O ILE A 48
SHEET 3 AA2 3 LEU A 76 GLN A 79 1 O ALA A 78 N VAL A 37
SHEET 1 AA3 2 GLU A 82 SER A 83 0
SHEET 2 AA3 2 LYS A 86 ALA A 87 -1 O LYS A 86 N SER A 83
SHEET 1 AA4 3 ILE A 319 ASN A 324 0
SHEET 2 AA4 3 GLU A 414 THR A 427 -1 O ALA A 426 N ILE A 319
SHEET 3 AA4 3 LEU A 331 THR A 333 -1 N ALA A 332 O TRP A 415
SHEET 1 AA5 4 ILE A 319 ASN A 324 0
SHEET 2 AA5 4 GLU A 414 THR A 427 -1 O ALA A 426 N ILE A 319
SHEET 3 AA5 4 GLN A 365 VAL A 372 -1 N VAL A 367 O CYS A 425
SHEET 4 AA5 4 LEU A 381 ALA A 386 -1 O ARG A 383 N VAL A 368
SHEET 1 AA6 2 ARG A 361 VAL A 362 0
SHEET 2 AA6 2 SER A 430 ALA A 431 -1 O SER A 430 N VAL A 362
LINK OD2AASP A 13 MN MN A 501 1555 1555 2.61
LINK OD2BASP A 13 MN MN A 501 1555 1555 2.07
LINK OD1AASP A 13 CA A CA A 502 1555 1555 2.16
LINK OD1BASP A 13 MN B MN A 503 1555 1555 2.19
LINK O MET A 14 CA A CA A 502 1555 1555 2.19
LINK O MET A 14 MN B MN A 503 1555 1555 2.20
LINK OD1 ASP A 115 MN MN A 501 1555 1555 2.24
LINK OD2 ASP A 115 CA A CA A 502 1555 1555 2.22
LINK OD2 ASP A 115 MN B MN A 503 1555 1555 2.21
LINK OE2 GLU A 116 MN MN A 501 1555 1555 2.19
LINK MN MN A 501 O1A DTP A 506 1555 1555 2.24
LINK MN MN A 501 O HOH A 791 1555 1555 2.21
LINK MN MN A 501 O3' DT P 8 1555 1555 2.36
LINK CA A CA A 502 O1B DTP A 506 1555 1555 2.28
LINK CA A CA A 502 O1A DTP A 506 1555 1555 2.43
LINK CA A CA A 502 O1G DTP A 506 1555 1555 2.23
LINK MN B MN A 503 O1B DTP A 506 1555 1555 2.28
LINK MN B MN A 503 O1A DTP A 506 1555 1555 2.42
LINK MN B MN A 503 O1G DTP A 506 1555 1555 2.24
CISPEP 1 LEU A 150 PRO A 151 0 2.06
CISPEP 2 LYS A 231 PRO A 232 0 1.26
CISPEP 3 LYS A 231 PRO A 232 0 -10.39
CISPEP 4 SER A 416 PRO A 417 0 -11.11
SITE 1 AC1 8 ASP A 13 ASP A 115 GLU A 116 CA A 502
SITE 2 AC1 8 MN A 503 DTP A 506 HOH A 791 DT P 8
SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 MN A 501
SITE 2 AC2 5 DTP A 506
SITE 1 AC3 5 ASP A 13 MET A 14 ASP A 115 MN A 501
SITE 2 AC3 5 DTP A 506
SITE 1 AC4 8 ARG A 24 GLN A 25 PRO A 244 SER A 248
SITE 2 AC4 8 GLY A 276 HOH A 629 HOH A 667 HOH A 679
SITE 1 AC5 11 ASN A 26 PRO A 27 HIS A 28 GLY A 271
SITE 2 AC5 11 ILE A 272 GLU A 273 TYR A 274 GLU A 277
SITE 3 AC5 11 HOH A 612 HOH A 621 HOH A 670
SITE 1 AC6 27 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC6 27 PHE A 17 PHE A 18 ILE A 48 ALA A 49
SITE 3 AC6 27 TYR A 52 ARG A 55 ARG A 61 ASP A 115
SITE 4 AC6 27 LYS A 231 MN A 501 CA A 502 MN A 503
SITE 5 AC6 27 HOH A 664 HOH A 697 HOH A 702 HOH A 770
SITE 6 AC6 27 HOH A 788 HOH A 791 DT P 8 HOH P 103
SITE 7 AC6 27 DT T 3 DT T 4 DA T 5
CRYST1 98.150 98.150 82.090 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 0.010188 0.005882 0.000000 0.00000
SCALE2 0.000000 0.011765 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012182 0.00000
(ATOM LINES ARE NOT SHOWN.)
END