HEADER TRANSFERASE/DNA 28-APR-10 3MR5
TITLE HUMAN DNA POLYMERASE ETA - DNA TERNARY COMPLEX WITH A CPD 1BP UPSTREAM
TITLE 2 OF THE ACTIVE SITE (TT3)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE ETA;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: CATALYTIC CORE (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*AP*CP*(TTD)P*AP*TP*GP*AP*CP*GP*A)-3');
COMPND 10 CHAIN: T;
COMPND 11 FRAGMENT: DNA TEMPLATE;
COMPND 12 ENGINEERED: YES;
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: DNA (5'-D(*AP*CP*GP*TP*CP*AP*TP*AP*A)-3');
COMPND 15 CHAIN: P;
COMPND 16 FRAGMENT: DNA PRIMER;
COMPND 17 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: 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 POL ETA, POLYMERASE, THYMINE DIMER, CPD, XPV, XERODERMA PIGMENTOSUM
KEYWDS 2 VARIANT, DNA DAMAGE, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR C.BIERTUMPFEL,Y.ZHAO,S.RAMON-MAIQUES,M.T.GREGORY,J.Y.LEE,W.YANG
REVDAT 4 03-APR-24 3MR5 1 REMARK
REVDAT 3 21-FEB-24 3MR5 1 REMARK SEQADV HETSYN LINK
REVDAT 2 21-MAR-12 3MR5 1 JRNL VERSN
REVDAT 1 30-JUN-10 3MR5 0
JRNL AUTH C.BIERTUMPFEL,Y.ZHAO,Y.KONDO,S.RAMON-MAIQUES,M.GREGORY,
JRNL AUTH 2 J.Y.LEE,C.MASUTANI,A.R.LEHMANN,F.HANAOKA,W.YANG
JRNL TITL STRUCTURE AND MECHANISM OF HUMAN DNA POLYMERASE ETA.
JRNL REF NATURE V. 465 1044 2010
JRNL REFN ISSN 0028-0836
JRNL PMID 20577208
JRNL DOI 10.1038/NATURE09196
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.2
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.96
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2042276.250
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.2
REMARK 3 NUMBER OF REFLECTIONS : 42013
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.191
REMARK 3 FREE R VALUE : 0.207
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700
REMARK 3 FREE R VALUE TEST SET COUNT : 3253
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6408
REMARK 3 BIN R VALUE (WORKING SET) : 0.2610
REMARK 3 BIN FREE R VALUE : 0.2880
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.20
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 576
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3347
REMARK 3 NUCLEIC ACID ATOMS : 395
REMARK 3 HETEROGEN ATOMS : 111
REMARK 3 SOLVENT ATOMS : 367
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 18.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.10
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.17000
REMARK 3 B22 (A**2) : -0.17000
REMARK 3 B33 (A**2) : 0.34000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20
REMARK 3 ESD FROM SIGMAA (A) : 0.18
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.22
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.200
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50
REMARK 3 IMPROPER ANGLES (DEGREES) : 2.150
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.240 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.920 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 1.890 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.840 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.40
REMARK 3 BSOL : 60.20
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : DNA-RNA_CB10.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 4 : ION.PARAM
REMARK 3 PARAMETER FILE 5 : LIGANDS0238.PARAM
REMARK 3 PARAMETER FILE 6 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_CB10.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER.TOP
REMARK 3 TOPOLOGY FILE 4 : ION.TOP
REMARK 3 TOPOLOGY FILE 5 : LIGANDS0238.TOP
REMARK 3 TOPOLOGY FILE 6 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4
REMARK 4 3MR5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-10.
REMARK 100 THE DEPOSITION ID IS D_1000058896.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-MAR-10
REMARK 200 TEMPERATURE (KELVIN) : 95
REMARK 200 PH : 6.0
REMARK 200 NUMBER OF CRYSTALS USED : NULL
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 : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42014
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 25.960
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 4.100
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06600
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1400
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6
REMARK 200 DATA REDUNDANCY IN SHELL : 4.10
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.57500
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: UNPUBLISHED STRUCTURE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.28
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 5 MM MGCL2, 6-21% (W/V) PEG
REMARK 280 2K-MME, STREAK/MICRO SEEDING, PH 6.0, VAPOR DIFFUSION, HANGING
REMARK 280 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 27.23433
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 54.46867
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 40.85150
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 68.08583
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 13.61717
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: 7790 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21030 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 THR A 156
REMARK 465 ALA A 157
REMARK 465 GLU A 158
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 LEU A 132 CG CD1 CD2
REMARK 470 THR A 155 OG1 CG2
REMARK 470 GLU A 159 CG CD OE1 OE2
REMARK 470 GLU A 335 CG CD OE1 OE2
REMARK 470 LYS A 376 CG CD CE NZ
REMARK 470 ILE A 411 CG1 CG2 CD1
REMARK 470 GLN A 412 CG CD OE1 NE2
REMARK 470 DT T 1 O5' C5' C4' O4' C3' C2' C1'
REMARK 470 DT T 1 N1 C2 O2 N3 C4 O4 C5
REMARK 470 DT T 1 C7 C6
REMARK 470 DA T 12 C5' C4' O4' C3' O3' C2' C1'
REMARK 470 DA T 12 N9 C8 N7 C5 C6 N6 N1
REMARK 470 DA T 12 C2 N3 C4
REMARK 470 DA P 1 O5' C5' C4' O4' C3' C2' C1'
REMARK 470 DA P 1 N9 C8 N7 C5 C6 N6 N1
REMARK 470 DA P 1 C2 N3 C4
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 61.92 24.21
REMARK 500 TYR A 39 161.68 70.31
REMARK 500 TYR A 39 116.69 69.88
REMARK 500 SER A 62 -2.23 85.86
REMARK 500 LEU A 183 -146.62 -115.18
REMARK 500 SER A 257 -2.40 85.94
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 444
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 434 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD1
REMARK 620 2 MET A 14 O 82.5
REMARK 620 3 ASP A 115 OD1 95.7 90.1
REMARK 620 4 XG4 A 433 O1B 166.2 92.5 97.2
REMARK 620 5 XG4 A 433 O1A 102.0 174.0 85.6 84.1
REMARK 620 6 XG4 A 433 O1G 84.7 93.1 176.8 82.8 91.3
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 435 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 13 OD2
REMARK 620 2 ASP A 115 OD2 96.9
REMARK 620 3 GLU A 116 OE2 91.2 91.5
REMARK 620 4 XG4 A 433 O1A 101.7 93.5 165.6
REMARK 620 5 HOH A 448 O 87.9 171.9 94.9 79.2
REMARK 620 6 DA P 9 O3' 171.7 85.6 80.8 86.0 90.5
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 XG4 A 433
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 434
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 435
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 436
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 437
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 438
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 439
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 440
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 441
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 442
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 443
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XG4 A 444
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 13
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 14
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL T 15
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: 3MR4 RELATED DB: PDB
REMARK 900 RELATED ID: 3MR6 RELATED DB: PDB
DBREF 3MR5 A 1 432 UNP Q9Y253 POLH_HUMAN 1 432
DBREF 3MR5 T 1 12 PDB 3MR5 3MR5 1 12
DBREF 3MR5 P 1 9 PDB 3MR5 3MR5 1 9
SEQADV 3MR5 GLY A -2 UNP Q9Y253 EXPRESSION TAG
SEQADV 3MR5 PRO A -1 UNP Q9Y253 EXPRESSION TAG
SEQADV 3MR5 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 DA DC TTD DA DT DG DA DC DG DA
SEQRES 1 P 9 DA DC DG DT DC DA DT DA DA
MODRES 3MR5 TTD T 5 DT CIS-SYN CYCLOBUTANE THYMINE DIMER
HET TTD T 5 40
HET XG4 A 433 31
HET MG A 434 1
HET MG A 435 1
HET GOL A 436 6
HET GOL A 437 6
HET GOL A 438 6
HET GOL A 439 6
HET GOL A 440 6
HET GOL A 441 6
HET GOL A 442 6
HET GOL A 443 6
HET XG4 A 444 12
HET GOL T 13 6
HET GOL T 14 6
HET GOL T 15 6
HETNAM TTD CIS-SYN CYCLOBUTANE THYMINE DIMER
HETNAM XG4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)
HETNAM 2 XG4 PHOSPHORYL]AMINO}PHOSPHORYL]GUANOSINE
HETNAM MG MAGNESIUM ION
HETNAM GOL GLYCEROL
HETSYN TTD [(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-DIHYDROXY-15A,
HETSYN 2 TTD 15B-DIMETHYL-7-OXIDO-13,15,16,18-
HETSYN 3 TTD TETRAOXOHEXADECAHYDRO-1H-1,4-EPOX Y-9,12-METHANO-6,8,
HETSYN 4 TTD 11-TRIOXA-12A,14,17,18A-TETRAAZA-7-
HETSYN 5 TTD PHOSPHACYCLOHEXADECA[1,2,3,4-DEF]BIPHENYLEN-10-
HETSYN 6 TTD YL]METHYL DIHYDROGEN PHOSPHATE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 TTD C20 H28 N4 O15 P2
FORMUL 4 XG4 2(C10 H17 N6 O12 P3)
FORMUL 5 MG 2(MG 2+)
FORMUL 7 GOL 11(C3 H8 O3)
FORMUL 19 HOH *367(H2 O)
HELIX 1 1 HIS A 0 GLY A 4 5 5
HELIX 2 2 CYS A 16 ASN A 26 1 11
HELIX 3 3 PRO A 27 ARG A 30 5 4
HELIX 4 4 SER A 51 ALA A 56 1 6
HELIX 5 5 TRP A 64 CYS A 72 1 9
HELIX 6 6 LEU A 89 ALA A 107 1 19
HELIX 7 7 LEU A 121 LYS A 131 1 11
HELIX 8 8 SER A 138 LEU A 142 5 5
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 239 GLY A 241 5 3
HELIX 13 13 SER A 242 GLN A 249 1 8
HELIX 14 14 MET A 250 ILE A 255 5 6
HELIX 15 15 GLY A 260 GLY A 271 1 12
HELIX 16 16 TYR A 274 PHE A 281 5 8
HELIX 17 17 THR A 282 GLY A 291 1 10
HELIX 18 18 GLY A 291 CYS A 302 1 12
HELIX 19 19 PRO A 326 ALA A 330 5 5
HELIX 20 20 ARG A 334 ASP A 360 1 27
HELIX 21 21 ASP A 391 LYS A 404 1 14
HELIX 22 22 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 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' DC T 4 P TTD T 5 1555 1555 1.61
LINK O3' TTD T 5 P DA T 6 1555 1555 1.61
LINK OD1 ASP A 13 MG MG A 434 1555 1555 2.03
LINK OD2 ASP A 13 MG MG A 435 1555 1555 1.97
LINK O MET A 14 MG MG A 434 1555 1555 2.11
LINK OD1 ASP A 115 MG MG A 434 1555 1555 2.07
LINK OD2 ASP A 115 MG MG A 435 1555 1555 2.08
LINK OE2 GLU A 116 MG MG A 435 1555 1555 2.12
LINK O1B XG4 A 433 MG MG A 434 1555 1555 2.19
LINK O1A XG4 A 433 MG MG A 434 1555 1555 2.22
LINK O1G XG4 A 433 MG MG A 434 1555 1555 2.30
LINK O1A XG4 A 433 MG MG A 435 1555 1555 2.28
LINK MG MG A 435 O HOH A 448 1555 1555 2.15
LINK MG MG A 435 O3' DA P 9 1555 1555 2.28
CISPEP 1 LEU A 150 PRO A 151 0 0.47
CISPEP 2 LYS A 231 PRO A 232 0 -0.09
CISPEP 3 SER A 416 PRO A 417 0 -0.60
SITE 1 AC1 28 ASP A 13 MET A 14 ASP A 15 CYS A 16
SITE 2 AC1 28 PHE A 17 PHE A 18 ILE A 48 ALA A 49
SITE 3 AC1 28 TYR A 52 ARG A 55 ARG A 61 ASP A 115
SITE 4 AC1 28 LYS A 231 MG A 434 MG A 435 HOH A 448
SITE 5 AC1 28 HOH A 466 HOH A 469 HOH A 480 HOH A 481
SITE 6 AC1 28 HOH A 544 HOH A 559 HOH A 610 HOH A 628
SITE 7 AC1 28 DA P 9 HOH P 18 DC T 4 TTD T 5
SITE 1 AC2 5 ASP A 13 MET A 14 ASP A 115 XG4 A 433
SITE 2 AC2 5 MG A 435
SITE 1 AC3 7 ASP A 13 ASP A 115 GLU A 116 XG4 A 433
SITE 2 AC3 7 MG A 434 HOH A 448 DA P 9
SITE 1 AC4 9 ARG A 24 GLN A 25 PRO A 244 SER A 248
SITE 2 AC4 9 GLY A 276 GLU A 277 GOL A 442 HOH A 452
SITE 3 AC4 9 HOH A 571
SITE 1 AC5 8 ARG A 55 ALA A 56 ARG A 361 PHE A 429
SITE 2 AC5 8 HOH A 493 HOH A 510 HOH A 517 HOH A 568
SITE 1 AC6 8 ASP A 13 GLU A 116 LYS A 224 CYS A 227
SITE 2 AC6 8 GLY A 228 HOH A 448 HOH A 480 HOH P 239
SITE 1 AC7 8 GLN A 20 GLN A 23 ARG A 24 ARG A 30
SITE 2 AC7 8 GLY A 209 HOH A 618 HOH A 647 HOH A 740
SITE 1 AC8 8 ILE A 147 GLU A 148 GLY A 149 LEU A 150
SITE 2 AC8 8 ARG A 389 HOH A 508 HOH A 532 HOH A 556
SITE 1 AC9 9 GLN A 5 THR A 184 ASP A 187 ARG A 206
SITE 2 AC9 9 GLU A 207 SER A 239 HIS A 240 GLY A 241
SITE 3 AC9 9 HOH A 485
SITE 1 BC1 10 HIS A 240 VAL A 243 PRO A 244 THR A 279
SITE 2 BC1 10 CYS A 302 ARG A 303 GOL A 436 HOH A 475
SITE 3 BC1 10 HOH A 571 HOH A 717
SITE 1 BC2 8 LYS A 224 ARG A 253 LYS A 254 ILE A 255
SITE 2 BC2 8 ARG A 256 GLY A 259 HOH A 464 DA P 8
SITE 1 BC3 6 SER A 257 LEU A 262 LYS A 293 ASN A 294
SITE 2 BC3 6 TRP A 297 HOH A 636
SITE 1 BC4 5 GLU A 82 ARG A 84 GLY A 85 DC T 10
SITE 2 BC4 5 DG T 11
SITE 1 BC5 2 TTD T 5 DA T 6
SITE 1 BC6 8 ALA A 112 HOH A 564 DA P 8 DA P 9
SITE 2 BC6 8 DA T 6 DT T 7 HOH T 17 HOH T 129
CRYST1 99.125 99.125 81.703 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 0.010088 0.005824 0.000000 0.00000
SCALE2 0.000000 0.011649 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012239 0.00000