HEADER TRANSFERASE/DNA 18-NOV-14 4RUC
TITLE CRYSTAL STRUCTURE OF Y-FAMILY DNA POLYMERASE DPO4 EXTENDING FROM A
TITLE 2 MEFAPY-DG:DC PAIR
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: NUCLEIC ACIDS TEMPLATE: TCAT(MF7)TAATCCTTCCCCC;
COMPND 9 CHAIN: T;
COMPND 10 ENGINEERED: YES;
COMPND 11 MOL_ID: 3;
COMPND 12 MOLECULE: NUCLEIC ACIDS PRIMAR: GGGGGAAGGATTAC;
COMPND 13 CHAIN: P;
COMPND 14 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS P2;
SOURCE 3 ORGANISM_TAXID: 273057;
SOURCE 4 STRAIN: ATCC 35092 / DSM 1617 / JCM 11322 / P2;
SOURCE 5 GENE: DBH, DPO4, SSO2448;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 11 ORGANISM_TAXID: 32630;
SOURCE 12 OTHER_DETAILS: CHEMICALLY SYNTHESIZED;
SOURCE 13 MOL_ID: 3;
SOURCE 14 SYNTHETIC: YES;
SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 16 ORGANISM_TAXID: 32630;
SOURCE 17 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS PROTEIN, DNA, DNA DAMAGE, DNA-DIRECTED DNA POLYMERASE, ADENOSINE
KEYWDS 2 TRIPHOSPHATE, Y-FAMILY POLYMERASE, TRANS-LESION SYNTHESIS (TLS), DNA
KEYWDS 3 BINDING, MEFAPY-DG LESION BYPASS, PRIMER EXTENSION, 2, 6-DIAMINO-4-
KEYWDS 4 HYDROXY N(5)-(METHYL)-FORMAMIDOPYRIMIDINE (MEFAPY-DG) LESION,
KEYWDS 5 TRANSFERASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PATRA,S.BANERJEE,M.P.STONE,M.EGLI
REVDAT 2 28-FEB-24 4RUC 1 REMARK LINK
REVDAT 1 05-AUG-15 4RUC 0
JRNL AUTH A.PATRA,S.BANERJEE,T.L.JOHNSON SALYARD,C.K.MALIK,
JRNL AUTH 2 P.P.CHRISTOV,C.J.RIZZO,M.P.STONE,M.EGLI
JRNL TITL STRUCTURAL BASIS FOR ERROR-FREE BYPASS OF THE
JRNL TITL 2 5-N-METHYLFORMAMIDOPYRIMIDINE-DG LESION BY HUMAN DNA
JRNL TITL 3 POLYMERASE ETA AND SULFOLOBUS SOLFATARICUS P2 POLYMERASE IV.
JRNL REF J.AM.CHEM.SOC. V. 137 7011 2015
JRNL REFN ISSN 0002-7863
JRNL PMID 25988947
JRNL DOI 10.1021/JACS.5B02701
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0073
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) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.88
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6
REMARK 3 NUMBER OF REFLECTIONS : 11228
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) : 0.175
REMARK 3 R VALUE (WORKING SET) : 0.172
REMARK 3 FREE R VALUE : 0.236
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 581
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) : 2.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98
REMARK 3 REFLECTION IN BIN (WORKING SET) : 708
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.18
REMARK 3 BIN R VALUE (WORKING SET) : 0.2690
REMARK 3 BIN FREE R VALUE SET COUNT : 40
REMARK 3 BIN FREE R VALUE : 0.3670
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2744
REMARK 3 NUCLEIC ACID ATOMS : 630
REMARK 3 HETEROGEN ATOMS : 33
REMARK 3 SOLVENT ATOMS : 58
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.84
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.75000
REMARK 3 B22 (A**2) : -0.95000
REMARK 3 B33 (A**2) : -1.80000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.388
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.298
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.157
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3509 ; 0.010 ; 0.018
REMARK 3 BOND LENGTHS OTHERS (A): 3211 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4846 ; 1.451 ; 1.838
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7416 ; 1.060 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 5.786 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;37.135 ;23.636
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 563 ;16.089 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.156 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 523 ; 0.075 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3419 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 750 ; 0.002 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
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): 1363 ; 4.327 ; 6.406
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1362 ; 4.317 ; 6.406
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1702 ; 6.421 ; 9.618
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1703 ; 6.899 ; 9.490
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2146 ; 5.901 ; 7.335
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2147 ; 6.400 ; 7.276
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3146 ; 9.851 ;10.655
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14619 ;13.504 ;63.265
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14600 ;13.497 ;63.268
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 : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
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 4RUC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-14.
REMARK 100 THE DEPOSITION ID IS D_1000087805.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-FEB-10
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0781
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11809
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 7.100
REMARK 200 R MERGE (I) : 0.14300
REMARK 200 R SYM (I) : 0.14300
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7150
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 7.10
REMARK 200 R MERGE FOR SHELL (I) : 0.61700
REMARK 200 R SYM FOR SHELL (I) : 0.61700
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.810
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER (MR)
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.43
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS HCL, PH 7.4, 15% PEG3350,
REMARK 280 100MM CALCIUM DIACETATE, 2.5% GLYCEROL , VAPOR DIFFUSION,
REMARK 280 HANGING DROP, TEMPERATURE 298K
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 47.19150
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.98600
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.19150
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.98600
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: 5680 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 20390 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 DT T 401
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 402 P OP1 OP2
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 DC T 402 N1 C2 C4
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 N MET A 1 O HOH A 2008 2.12
REMARK 500 O HOH A 2013 O HOH A 2025 2.17
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 MF7 T 405 O3' DT T 406 P -0.404
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 ARG A 336 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES
REMARK 500 MF7 T 405 C3' - O3' - P ANGL. DEV. = 40.0 DEGREES
REMARK 500 DT T 406 O3' - P - O5' ANGL. DEV. = 12.8 DEGREES
REMARK 500 DT T 406 O3' - P - OP2 ANGL. DEV. = -20.4 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 50.12 31.19
REMARK 500 ASN A 20 79.15 -151.28
REMARK 500 ARG A 36 -95.94 -77.37
REMARK 500 SER A 103 -178.67 -172.41
REMARK 500 ASP A 113 38.79 -84.85
REMARK 500 LYS A 114 -55.46 -146.98
REMARK 500 SER A 145 -160.24 -163.24
REMARK 500 SER A 207 -32.05 -34.21
REMARK 500 ASN A 234 54.39 -162.06
REMARK 500 ASP A 277 88.81 43.89
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 402 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD2
REMARK 620 2 ASP A 105 OD2 64.0
REMARK 620 3 GLU A 106 OE2 97.1 107.8
REMARK 620 4 DTP A 401 O1A 83.1 68.7 176.1
REMARK 620 5 DC P 514 O5' 162.8 130.7 71.1 109.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 403 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 7 OD1
REMARK 620 2 ASP A 7 OD2 44.7
REMARK 620 3 PHE A 8 O 67.7 103.1
REMARK 620 4 ASP A 105 OD1 100.3 88.5 69.3
REMARK 620 5 ASP A 105 OD2 89.7 52.8 106.9 47.0
REMARK 620 6 DTP A 401 O3G 74.7 93.9 100.4 169.7 140.5
REMARK 620 7 DTP A 401 O1A 114.9 76.9 174.2 104.9 68.3 85.4
REMARK 620 8 DTP A 401 O1B 153.4 158.6 97.9 94.6 116.3 86.8 81.8
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 404 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ALA A 181 O
REMARK 620 2 ILE A 186 O 87.1
REMARK 620 3 HOH A2004 O 69.7 61.6
REMARK 620 4 HOH A2005 O 67.0 141.7 82.6
REMARK 620 5 HOH P 601 O 132.7 88.9 67.1 89.0
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTP A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 404
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4RU9 RELATED DB: PDB
REMARK 900 RELATED ID: 4RUA RELATED DB: PDB
DBREF 4RUC A 1 341 UNP Q97W02 DPO4_SULSO 1 341
DBREF 4RUC T 401 418 PDB 4RUC 4RUC 401 418
DBREF 4RUC P 501 514 PDB 4RUC 4RUC 501 514
SEQRES 1 A 341 MET 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 T 18 DT DC DA DT MF7 DT DA DA DT DC DC DT DT
SEQRES 2 T 18 DC DC DC DC DC
SEQRES 1 P 14 DG DG DG DG DG DA DA DG DG DA DT DT DA
SEQRES 2 P 14 DC
HET MF7 T 405 24
HET DTP A 401 30
HET CA A 402 1
HET CA A 403 1
HET CA A 404 1
HETNAM MF7 N-{2-AMINO-5-[FORMYL(METHYL)AMINO]-6-HYDROXYPYRIMIDIN-
HETNAM 2 MF7 4-YL}-2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-
HETNAM 3 MF7 PENTOFURANOSYLAMINE
HETNAM DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
HETNAM CA CALCIUM ION
FORMUL 2 MF7 C11 H18 N5 O8 P
FORMUL 4 DTP C10 H16 N5 O12 P3
FORMUL 5 CA 3(CA 2+)
FORMUL 8 HOH *58(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 LYS A 52 1 6
HELIX 4 4 PRO A 60 LEU A 68 1 9
HELIX 5 5 ARG A 77 ARG A 93 1 17
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 ASP A 167 LEU A 178 1 12
HELIX 9 9 ASP A 179 VAL A 183 5 5
HELIX 10 10 GLY A 187 LEU A 197 1 11
HELIX 11 11 LYS A 201 LEU A 206 5 6
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 ILE A 101 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 VAL A 6 O ALA A 107
SHEET 4 A 5 VAL A 140 SER A 145 -1 O SER A 145 N VAL A 3
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 LEU A 74 N CYS A 31
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' DT T 404 P1 MF7 T 405 1555 1555 1.60
LINK O3' MF7 T 405 P DT T 406 1555 1555 1.20
LINK OD2 ASP A 7 CA CA A 402 1555 1555 2.52
LINK OD1 ASP A 7 CA CA A 403 1555 1555 2.47
LINK OD2 ASP A 7 CA CA A 403 1555 1555 3.15
LINK O PHE A 8 CA CA A 403 1555 1555 2.27
LINK OD2 ASP A 105 CA CA A 402 1555 1555 2.57
LINK OD1 ASP A 105 CA CA A 403 1555 1555 2.50
LINK OD2 ASP A 105 CA CA A 403 1555 1555 2.91
LINK OE2 GLU A 106 CA CA A 402 1555 1555 2.58
LINK O ALA A 181 CA CA A 404 1555 1555 2.38
LINK O ILE A 186 CA CA A 404 1555 1555 2.73
LINK O1A DTP A 401 CA CA A 402 1555 1555 2.62
LINK O3G DTP A 401 CA CA A 403 1555 1555 2.08
LINK O1A DTP A 401 CA CA A 403 1555 1555 2.20
LINK O1B DTP A 401 CA CA A 403 1555 1555 2.32
LINK CA CA A 402 O5' DC P 514 1555 1555 3.12
LINK CA CA A 404 O HOH A2004 1555 1555 2.42
LINK CA CA A 404 O HOH A2005 1555 1555 2.42
LINK CA CA A 404 O HOH P 601 1555 1555 2.53
CISPEP 1 LYS A 159 PRO A 160 0 2.95
SITE 1 AC1 16 ASP A 7 PHE A 8 TYR A 10 PHE A 11
SITE 2 AC1 16 TYR A 12 ALA A 44 THR A 45 TYR A 48
SITE 3 AC1 16 ARG A 51 ASP A 105 LYS A 159 CA A 402
SITE 4 AC1 16 CA A 403 DC P 514 DT T 404 MF7 T 405
SITE 1 AC2 5 ASP A 7 ASP A 105 GLU A 106 DTP A 401
SITE 2 AC2 5 DC P 514
SITE 1 AC3 4 ASP A 7 PHE A 8 ASP A 105 DTP A 401
SITE 1 AC4 7 ALA A 181 VAL A 183 ILE A 186 HOH A2004
SITE 2 AC4 7 HOH A2005 DA P 513 HOH P 601
CRYST1 94.383 103.972 52.563 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 0.010595 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009618 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019025 0.00000