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 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 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