HEADER TRANSFERASE/DNA 05-MAR-09 3GII
TITLE DPO4 EXTENSION TERNARY COMPLEX WITH DISORDERED A OPPOSITE AN OXOG IN
TITLE 2 ANTI CONFORMATION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA POLYMERASE IV;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: POL IV;
COMPND 5 EC: 2.7.7.7;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3';
COMPND 9 CHAIN: D;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: 5'-D(*CP*TP*AP*AP*CP*(8OG)
COMPND 13 P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3';
COMPND 14 CHAIN: E;
COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS P2;
SOURCE 3 ORGANISM_TAXID: 273057;
SOURCE 4 STRAIN: P2 / DSM 1617 / JCM 11322;
SOURCE 5 ATCC: 35092;
SOURCE 6 GENE: DBH, DPO4, SSO2448;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL(STRATAGENE);
SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A;
SOURCE 12 MOL_ID: 2;
SOURCE 13 SYNTHETIC: YES;
SOURCE 14 OTHER_DETAILS: DNA PRIMER;
SOURCE 15 MOL_ID: 3;
SOURCE 16 SYNTHETIC: YES;
SOURCE 17 OTHER_DETAILS: OXOG-MODIFIED TEMPLATE STRAND
KEYWDS DNA POLYMERASE, 8-OXOGUANINE, Y-FAMILY, LESION BYPASS, DNA DAMAGE,
KEYWDS 2 DNA REPAIR, DNA REPLICATION, DNA-BINDING, DNA-DIRECTED DNA
KEYWDS 3 POLYMERASE, MAGNESIUM, METAL-BINDING, MUTATOR PROTEIN,
KEYWDS 4 NUCLEOTIDYLTRANSFERASE, TRANSFERASE, TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR O.RECHKOBLIT,L.MALININA,D.J.PATEL
REVDAT 4 06-SEP-23 3GII 1 REMARK DBREF SEQADV LINK
REVDAT 3 07-DEC-11 3GII 1 JRNL
REVDAT 2 13-JUL-11 3GII 1 VERSN
REVDAT 1 19-MAY-09 3GII 0
JRNL AUTH O.RECHKOBLIT,L.MALININA,Y.CHENG,N.E.GEACINTOV,S.BROYDE,
JRNL AUTH 2 D.J.PATEL
JRNL TITL IMPACT OF CONFORMATIONAL HETEROGENEITY OF OXOG LESIONS AND
JRNL TITL 2 THEIR PAIRING PARTNERS ON BYPASS FIDELITY BY Y FAMILY
JRNL TITL 3 POLYMERASES.
JRNL REF STRUCTURE V. 17 725 2009
JRNL REFN ISSN 0969-2126
JRNL PMID 19446528
JRNL DOI 10.1016/J.STR.2009.03.011
REMARK 2
REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2
REMARK 3 NUMBER OF REFLECTIONS : 16924
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 + TEST SET) : 0.205
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.265
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 856
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67
REMARK 3 REFLECTION IN BIN (WORKING SET) : 880
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.56
REMARK 3 BIN R VALUE (WORKING SET) : 0.3340
REMARK 3 BIN FREE R VALUE SET COUNT : 41
REMARK 3 BIN FREE R VALUE : 0.4420
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2740
REMARK 3 NUCLEIC ACID ATOMS : 628
REMARK 3 HETEROGEN ATOMS : 35
REMARK 3 SOLVENT ATOMS : 66
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.03
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 5.08000
REMARK 3 B22 (A**2) : -1.85000
REMARK 3 B33 (A**2) : -3.24000
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 OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.687
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.332
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.242
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.176
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3525 ; 0.010 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2294 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4866 ; 1.651 ; 2.227
REMARK 3 BOND ANGLES OTHERS (DEGREES): 5623 ; 0.923 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 5.248 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;34.715 ;23.636
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 560 ;17.969 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.422 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.110 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3332 ; 0.004 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 556 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 687 ; 0.213 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2381 ; 0.195 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1629 ; 0.191 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 1726 ; 0.082 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 106 ; 0.190 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.004 ; 0.200
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.261 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.267 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 19 ; 0.225 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.142 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1707 ; 0.472 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 688 ; 0.063 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2759 ; 0.843 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1968 ; 1.152 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2107 ; 1.837 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 341
REMARK 3 ORIGIN FOR THE GROUP (A): 21.4417 17.4027 12.4807
REMARK 3 T TENSOR
REMARK 3 T11: -0.1140 T22: -0.0849
REMARK 3 T33: -0.1157 T12: 0.0174
REMARK 3 T13: -0.0474 T23: -0.0030
REMARK 3 L TENSOR
REMARK 3 L11: 0.6746 L22: 2.3402
REMARK 3 L33: 1.9552 L12: -0.1814
REMARK 3 L13: -0.0155 L23: -0.5731
REMARK 3 S TENSOR
REMARK 3 S11: -0.0266 S12: -0.0681 S13: 0.0519
REMARK 3 S21: -0.0284 S22: 0.0675 S23: 0.1591
REMARK 3 S31: -0.1566 S32: -0.3078 S33: -0.0409
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 2
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : D 802 D 813
REMARK 3 RESIDUE RANGE : E 901 E 919
REMARK 3 ORIGIN FOR THE GROUP (A): 10.0145 9.4844 22.9242
REMARK 3 T TENSOR
REMARK 3 T11: -0.0433 T22: 0.1532
REMARK 3 T33: 0.0453 T12: -0.0524
REMARK 3 T13: 0.0475 T23: 0.0480
REMARK 3 L TENSOR
REMARK 3 L11: 2.4648 L22: 3.5787
REMARK 3 L33: 1.4284 L12: -0.8044
REMARK 3 L13: 0.4767 L23: -0.5319
REMARK 3 S TENSOR
REMARK 3 S11: 0.1084 S12: -0.4557 S13: 0.2268
REMARK 3 S21: 0.4797 S22: 0.1497 S23: 0.6500
REMARK 3 S31: -0.0927 S32: -0.6972 S33: -0.2581
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3GII COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-09.
REMARK 100 THE DEPOSITION ID IS D_1000051902.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 22-NOV-05
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97942
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : 6144 X 6144 PIXEL ELEMENTS WITH
REMARK 200 AN EFFECTIVE PIXEL SIZE LESS
REMARK 200 THAN 60X60 MICRON AND RESOLUTION
REMARK 200 OF ORDER 90X90 MICRON
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16924
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2
REMARK 200 DATA REDUNDANCY : 6.200
REMARK 200 R MERGE (I) : 0.09600
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67
REMARK 200 COMPLETENESS FOR SHELL (%) : 71.7
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.52800
REMARK 200 R SYM FOR SHELL (I) : NULL
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: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 2ASD
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 57.47
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 100 MM CALCIUM ACETATE,
REMARK 280 10% PEG 4000, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X+1/2,Y+1/2,-Z
REMARK 290 4555 X+1/2,-Y+1/2,-Z
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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 47.88050
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.82300
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.88050
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.82300
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
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: 4210 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.8 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D, E
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 2DA D 814
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 DT D 803 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DT D 808 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES
REMARK 500 DT D 808 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DG D 809 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG D 813 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DC E 901 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES
REMARK 500 DT E 908 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DC E 914 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES
REMARK 500 DC E 914 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DC E 914 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DC E 915 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES
REMARK 500 DC E 915 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES
REMARK 500 DA E 917 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 DC E 918 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES
REMARK 500 DC E 919 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 TYR A 10 56.32 21.10
REMARK 500 PHE A 37 -179.24 -170.72
REMARK 500 ASN A 161 44.29 38.54
REMARK 500 LYS A 196 44.01 -74.88
REMARK 500 LEU A 197 -7.82 -179.41
REMARK 500 SER A 207 41.00 -104.98
REMARK 500 LYS A 278 -16.63 79.93
REMARK 500 LYS A 339 65.75 60.55
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 CA A 415 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD1
REMARK 620 2 ASP A 105 OD1 88.7
REMARK 620 3 ASP A 105 OD2 65.7 44.2
REMARK 620 4 GLU A 106 OE2 87.4 91.8 125.3
REMARK 620 5 DGT A 414 O2A 88.4 99.1 62.2 168.3
REMARK 620 6 HOH A 599 O 165.7 79.0 108.6 85.8 100.6
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 416 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD1
REMARK 620 2 ASP A 7 OD2 48.1
REMARK 620 3 PHE A 8 O 109.7 84.4
REMARK 620 4 ASP A 105 OD2 70.5 107.8 84.2
REMARK 620 5 DGT A 414 O1G 108.2 82.6 113.5 160.7
REMARK 620 6 DGT A 414 O1B 151.7 159.9 86.8 89.2 84.3
REMARK 620 7 DGT A 414 O2A 75.5 111.9 159.1 78.4 82.6 81.4
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 420 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 169 OE2
REMARK 620 2 HOH A 421 O 106.9
REMARK 620 3 HOH A 422 O 48.6 127.4
REMARK 620 4 HOH A 425 O 67.6 66.8 60.8
REMARK 620 5 HOH A 426 O 99.0 87.0 135.3 143.8
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 417 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 181 O
REMARK 620 2 VAL A 183 O 97.0
REMARK 620 3 ILE A 186 O 95.3 91.3
REMARK 620 4 HOH A 576 O 65.2 161.4 85.5
REMARK 620 5 HOH D 582 O 98.8 73.3 160.2 113.1
REMARK 620 6 DG D 813 OP1 164.6 73.1 96.7 125.4 67.4
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 DGT A 414
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 415
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 416
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 417
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 420
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2ASD RELATED DB: PDB
REMARK 900 OXOG-MODIFIED DPO4 INSERTION TERNARY COMPLEX
REMARK 900 RELATED ID: 2ASJ RELATED DB: PDB
REMARK 900 OXOG-MODIFIED DPO4 PRE-INSERTION BINARY COMPLEX
REMARK 900 RELATED ID: 2ASL RELATED DB: PDB
REMARK 900 OXOG-MODIFIED DPO4 POST-INSERTION BINARY COMPLEX
REMARK 900 RELATED ID: 3GIJ RELATED DB: PDB
REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH OXOG(SYN)-A(ANTI) AND OXOG(ANTI)
REMARK 900 -A(SYN) PAIRS
REMARK 900 RELATED ID: 3GIK RELATED DB: PDB
REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH THE OXOG(ANTI)-C(ANTI) PAIR
REMARK 900 RELATED ID: 3GIL RELATED DB: PDB
REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH OXOG(ANTI)-T(ANTI) PAIR
REMARK 900 RELATED ID: 3GIM RELATED DB: PDB
REMARK 900 DPO4 EXTENSION TERNARY COMPLEX WITH OXOG(ANTI)-G(SYN) PAIR
DBREF 3GII A 2 341 UNP Q97W02 DPO42_SULSO 2 341
DBREF 3GII D 802 814 PDB 3GII 3GII 802 814
DBREF 3GII E 901 919 PDB 3GII 3GII 901 919
SEQADV 3GII GLY A 1 UNP Q97W02 EXPRESSION TAG
SEQRES 1 A 341 GLY ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA
SEQRES 2 A 341 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS
SEQRES 3 A 341 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP
SEQRES 4 A 341 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS
SEQRES 5 A 341 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS
SEQRES 6 A 341 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS
SEQRES 7 A 341 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU
SEQRES 8 A 341 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE
SEQRES 9 A 341 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP
SEQRES 10 A 341 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN
SEQRES 11 A 341 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY
SEQRES 12 A 341 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP
SEQRES 13 A 341 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU
SEQRES 14 A 341 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP
SEQRES 15 A 341 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS
SEQRES 16 A 341 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE
SEQRES 17 A 341 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS
SEQRES 18 A 341 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN
SEQRES 19 A 341 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG
SEQRES 20 A 341 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU
SEQRES 21 A 341 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR
SEQRES 22 A 341 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL
SEQRES 23 A 341 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY
SEQRES 24 A 341 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR
SEQRES 25 A 341 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU
SEQRES 26 A 341 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER
SEQRES 27 A 341 LYS PHE ILE
SEQRES 1 D 13 DG DT DT DG DG DA DT DG DG DT DA DG 2DA
SEQRES 1 E 19 DC DT DA DA DC 8OG DC DT DA DC DC DA DT
SEQRES 2 E 19 DC DC DA DA DC DC
MODRES 3GII 8OG E 906 DG
HET 8OG E 906 23
HET DGT A 414 31
HET CA A 415 1
HET CA A 416 1
HET CA A 417 1
HET NA A 420 1
HETNAM 8OG 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
HETNAM CA CALCIUM ION
HETNAM NA SODIUM ION
HETSYN 8OG 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
FORMUL 3 8OG C10 H14 N5 O8 P
FORMUL 4 DGT C10 H16 N5 O13 P3
FORMUL 5 CA 3(CA 2+)
FORMUL 8 NA NA 1+
FORMUL 9 HOH *66(H2 O)
HELIX 1 1 TYR A 10 ASN A 20 1 11
HELIX 2 2 PRO A 21 LYS A 24 5 4
HELIX 3 3 ASN A 47 PHE A 53 1 7
HELIX 4 4 PRO A 60 LEU A 68 1 9
HELIX 5 5 ARG A 77 GLU A 94 1 18
HELIX 6 6 ASP A 117 LYS A 137 1 21
HELIX 7 7 ASN A 147 LYS A 159 1 13
HELIX 8 8 GLU A 169 LEU A 178 1 10
HELIX 9 9 ASP A 179 VAL A 183 5 5
HELIX 10 10 GLY A 187 LYS A 196 1 10
HELIX 11 11 LYS A 201 ILE A 208 5 8
HELIX 12 12 GLU A 209 GLY A 218 1 10
HELIX 13 13 GLY A 218 ARG A 230 1 13
HELIX 14 14 ASN A 257 ASP A 277 1 21
HELIX 15 15 SER A 307 ASP A 326 1 20
SHEET 1 A 5 ILE A 99 SER A 103 0
SHEET 2 A 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100
SHEET 3 A 5 VAL A 3 PHE A 8 -1 N LEU A 4 O LEU A 109
SHEET 4 A 5 VAL A 140 SER A 145 -1 O GLY A 143 N PHE A 5
SHEET 5 A 5 ILE A 163 VAL A 165 1 O LYS A 164 N ILE A 144
SHEET 1 B 3 GLY A 41 ALA A 46 0
SHEET 2 B 3 VAL A 28 PHE A 33 -1 N VAL A 32 O ALA A 42
SHEET 3 B 3 VAL A 72 PRO A 75 1 O VAL A 72 N VAL A 29
SHEET 1 C 4 SER A 244 SER A 255 0
SHEET 2 C 4 ILE A 330 PHE A 340 -1 O PHE A 337 N ILE A 245
SHEET 3 C 4 PRO A 281 THR A 290 -1 N VAL A 289 O ARG A 331
SHEET 4 C 4 ILE A 295 THR A 301 -1 O ARG A 298 N VAL A 286
LINK O3' DC E 905 P 8OG E 906 1555 1555 1.60
LINK O3' 8OG E 906 P DC E 907 1555 1555 1.59
LINK OD1 ASP A 7 CA CA A 415 1555 1555 2.32
LINK OD1 ASP A 7 CA CA A 416 1555 1555 2.91
LINK OD2 ASP A 7 CA CA A 416 1555 1555 2.32
LINK O PHE A 8 CA CA A 416 1555 1555 2.32
LINK OD1 ASP A 105 CA CA A 415 1555 1555 2.39
LINK OD2 ASP A 105 CA CA A 415 1555 1555 3.16
LINK OD2 ASP A 105 CA CA A 416 1555 1555 2.31
LINK OE2 GLU A 106 CA CA A 415 1555 1555 2.32
LINK OE2 GLU A 169 NA NA A 420 1555 1555 2.23
LINK O ALA A 181 CA CA A 417 1555 1555 2.30
LINK O VAL A 183 CA CA A 417 1555 1555 3.04
LINK O ILE A 186 CA CA A 417 1555 1555 2.28
LINK O2A DGT A 414 CA CA A 415 1555 1555 2.32
LINK O1G DGT A 414 CA CA A 416 1555 1555 2.71
LINK O1B DGT A 414 CA CA A 416 1555 1555 2.34
LINK O2A DGT A 414 CA CA A 416 1555 1555 2.31
LINK CA CA A 415 O HOH A 599 1555 1555 2.80
LINK CA CA A 417 O HOH A 576 1555 1555 2.53
LINK CA CA A 417 O HOH D 582 1555 1555 2.41
LINK CA CA A 417 OP1 DG D 813 1555 1555 3.20
LINK NA NA A 420 O HOH A 421 1555 1555 2.32
LINK NA NA A 420 O HOH A 422 1555 1555 2.93
LINK NA NA A 420 O HOH A 425 1555 1555 2.56
LINK NA NA A 420 O HOH A 426 1555 1555 2.98
CISPEP 1 LYS A 159 PRO A 160 0 2.63
SITE 1 AC1 15 ASP A 7 PHE A 8 TYR A 10 PHE A 11
SITE 2 AC1 15 TYR A 12 ALA A 44 THR A 45 TYR A 48
SITE 3 AC1 15 ARG A 51 ASP A 105 LYS A 159 CA A 415
SITE 4 AC1 15 CA A 416 DC E 905 8OG E 906
SITE 1 AC2 6 ASP A 7 ASP A 105 GLU A 106 DGT A 414
SITE 2 AC2 6 CA A 416 HOH A 599
SITE 1 AC3 5 ASP A 7 PHE A 8 ASP A 105 DGT A 414
SITE 2 AC3 5 CA A 415
SITE 1 AC4 6 ALA A 181 VAL A 183 ILE A 186 HOH A 576
SITE 2 AC4 6 HOH D 582 DG D 813
SITE 1 AC5 6 GLU A 169 HOH A 421 HOH A 422 HOH A 423
SITE 2 AC5 6 HOH A 425 HOH A 426
CRYST1 95.761 111.646 52.708 90.00 90.00 90.00 P 21 21 2 4
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 0.010443 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008957 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018972 0.00000
(ATOM LINES ARE NOT SHOWN.)
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