HEADER HYDROLASE 27-MAR-09 2WE3 TITLE EBV DUTPASE INACTIVE MUTANT DELETED OF MOTIF V COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-256; COMPND 5 SYNONYM: DUTP PYROPHOSPHATASE, DUTPASE; COMPND 6 EC: 3.6.1.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN HERPESVIRUS 4; SOURCE 3 ORGANISM_COMMON: EPSTEIN-BARR VIRUS; SOURCE 4 ORGANISM_TAXID: 10377; SOURCE 5 STRAIN: B95-8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEX HTB KEYWDS DUTPASE, MONOMER, HYDROLASE, HUMAN HERPES VIRUS, EPSTEIN-BARR VIRUS, KEYWDS 2 NUCLEOTIDE METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR L.FREEMAN,M.BUISSON,N.TARBOURIECH,W.P.BURMEISTER REVDAT 5 09-OCT-24 2WE3 1 REMARK REVDAT 4 13-DEC-23 2WE3 1 REMARK LINK REVDAT 3 15-SEP-09 2WE3 1 JRNL DBREF REVDAT 2 21-JUL-09 2WE3 1 JRNL REVDAT 1 07-JUL-09 2WE3 0 JRNL AUTH L.FREEMAN,M.BUISSON,N.TARBOURIECH,A.VAN DER HEYDEN,P.LABBE, JRNL AUTH 2 W.P.BURMEISTER JRNL TITL THE FLEXIBLE MOTIF V OF EPSTEIN-BARR VIRUS DEOXYURIDINE JRNL TITL 2 5'-TRIPHOSPHATE PYROPHOSPHATASE IS ESSENTIAL FOR CATALYSIS. JRNL REF J.BIOL.CHEM. V. 284 25280 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19586911 JRNL DOI 10.1074/JBC.M109.019315 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.TARBOURIECH,M.BUISSON,J.M.SEIGNEURIN,S.CUSACK, REMARK 1 AUTH 2 W.P.BURMEISTER REMARK 1 TITL THE MONOMERIC DUTPASE FROM EPSTEIN-BARR VIRUS MIMICS REMARK 1 TITL 2 TRIMERIC DUTPASES REMARK 1 REF STRUCTURE V. 13 1299 2005 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 16154087 REMARK 1 DOI 10.1016/J.STR.2005.06.009 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0038 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 16194 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 865 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1171 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1903 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.06000 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): 0.217 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.197 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.421 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2008 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2740 ; 1.719 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 241 ; 6.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;27.586 ;21.341 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 323 ;17.428 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;23.896 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 305 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1493 ; 0.007 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1206 ; 0.893 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1965 ; 1.638 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 802 ; 2.465 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 773 ; 3.992 ; 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 : 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 2WE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290039040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9395 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17157 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 72.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2BSY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 20 % PEG 3350, 200 REMARK 280 MM LISO4, AND 10 MM DUTP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.61900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.61900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.84850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.61900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.61900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.84850 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 51.61900 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 51.61900 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 23.84850 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 51.61900 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 51.61900 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 23.84850 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -7 REMARK 465 ALA A -6 REMARK 465 MET A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 GLY A -2 REMARK 465 ILE A -1 REMARK 465 PRO A 0 REMARK 465 ALA A 21 REMARK 465 SER A 22 REMARK 465 VAL A 23 REMARK 465 MET A 116 REMARK 465 GLU A 117 REMARK 465 GLU A 118 REMARK 465 ASP A 119 REMARK 465 LYS A 120 REMARK 465 GLY A 121 REMARK 465 PRO A 122 REMARK 465 ILE A 123 REMARK 465 ASN A 124 REMARK 465 HIS A 125 REMARK 465 PRO A 126 REMARK 465 GLN A 127 REMARK 465 TYR A 128 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 ASP A 14 OD1 OD2 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 O HOH A 2021 O HOH A 2022 1.96 REMARK 500 O3 SO4 A 1260 O HOH A 2084 2.06 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 84 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 6 153.97 -47.67 REMARK 500 ASN A 13 113.18 -172.21 REMARK 500 SER A 100 -10.90 73.50 REMARK 500 ASP A 131 151.70 -35.71 REMARK 500 HIS A 163 9.19 88.73 REMARK 500 LYS A 207 137.23 -39.82 REMARK 500 TYR A 208 -4.19 76.74 REMARK 500 CYS A 212 -173.53 -170.49 REMARK 500 TYR A 226 93.64 -69.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 255 MET A 256 -148.99 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 MG A1258 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DUT A1257 O2A REMARK 620 2 DUT A1257 O2B 89.1 REMARK 620 3 DUT A1257 O2G 95.4 90.2 REMARK 620 4 HOH A2046 O 98.4 90.3 166.1 REMARK 620 5 HOH A2048 O 179.2 91.2 83.8 82.3 REMARK 620 6 HOH A2082 O 92.0 177.0 87.0 92.3 87.7 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUT A 1257 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1260 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BSY RELATED DB: PDB REMARK 900 EPSTEIN BARR VIRUS DUTPASE REMARK 900 RELATED ID: 2WE0 RELATED DB: PDB REMARK 900 EBV DUTPASE MUTANT CYS4SER REMARK 900 RELATED ID: 2WE1 RELATED DB: PDB REMARK 900 EBV DUTPASE MUTANT ASP131ASN WITH BOUND DUMP REMARK 900 RELATED ID: 2BT1 RELATED DB: PDB REMARK 900 EPSTEIN BARR VIRUS DUTPASE IN COMPLEX WITH A,B-IMINO DUTP REMARK 900 RELATED ID: 2WE2 RELATED DB: PDB REMARK 900 EBV DUTPASE DOUBLE MUTANT GLY78ASP-ASP131SER WITH DUMP DBREF 2WE3 A -7 0 PDB 2WE3 2WE3 -7 0 DBREF 2WE3 A 1 256 UNP P03195 DUT_EBVB9 1 256 SEQRES 1 A 264 GLY ALA MET GLY SER GLY ILE PRO MET GLU ALA CYS PRO SEQRES 2 A 264 HIS ILE ARG TYR ALA PHE GLN ASN ASP LYS LEU LEU LEU SEQRES 3 A 264 GLN GLN ALA SER VAL GLY ARG LEU THR LEU VAL ASN LYS SEQRES 4 A 264 THR THR ILE LEU LEU ARG PRO MET LYS THR THR THR VAL SEQRES 5 A 264 ASP LEU GLY LEU TYR ALA ARG PRO PRO GLU GLY HIS GLY SEQRES 6 A 264 LEU MET LEU TRP GLY SER THR SER ARG PRO VAL THR SER SEQRES 7 A 264 HIS VAL GLY ILE ILE ASP PRO GLY TYR THR GLY GLU LEU SEQRES 8 A 264 ARG LEU ILE LEU GLN ASN GLN ARG ARG TYR ASN SER THR SEQRES 9 A 264 LEU ARG PRO SER GLU LEU LYS ILE HIS LEU ALA ALA PHE SEQRES 10 A 264 ARG TYR ALA THR PRO GLN MET GLU GLU ASP LYS GLY PRO SEQRES 11 A 264 ILE ASN HIS PRO GLN TYR PRO GLY ASP VAL GLY LEU ASP SEQRES 12 A 264 VAL SER LEU PRO LYS ASP LEU ALA LEU PHE PRO HIS GLN SEQRES 13 A 264 THR VAL SER VAL THR LEU THR VAL PRO PRO PRO SER ILE SEQRES 14 A 264 PRO HIS HIS ARG PRO THR ILE PHE GLY ARG SER GLY LEU SEQRES 15 A 264 ALA MET GLN GLY ILE LEU VAL LYS PRO CYS ARG TRP ARG SEQRES 16 A 264 ARG GLY GLY VAL ASP VAL SER LEU THR ASN PHE SER ASP SEQRES 17 A 264 GLN THR VAL PHE LEU ASN LYS TYR ARG ARG PHE CYS GLN SEQRES 18 A 264 LEU VAL TYR LEU HIS LYS HIS HIS LEU THR SER PHE TYR SEQRES 19 A 264 SER PRO HIS SER ASP ALA GLY VAL LEU GLY PRO ARG SER SEQRES 20 A 264 LEU PHE ARG TRP ALA SER CYS THR PHE GLU GLU VAL PRO SEQRES 21 A 264 SER LEU ALA MET HET DUT A1257 28 HET MG A1258 1 HET SO4 A1259 5 HET SO4 A1260 5 HETNAM DUT DEOXYURIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 2 DUT C9 H15 N2 O14 P3 FORMUL 3 MG MG 2+ FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *84(H2 O) HELIX 1 1 ARG A 171 GLN A 177 1 7 HELIX 2 2 PRO A 252 ALA A 255 5 4 SHEET 1 AA 5 VAL A 68 SER A 70 0 SHEET 2 AA 5 LEU A 83 ASN A 89 -1 O GLN A 88 N THR A 69 SHEET 3 AA 5 THR A 41 ARG A 51 -1 O THR A 42 N LEU A 87 SHEET 4 AA 5 ILE A 7 PHE A 11 -1 O ARG A 8 N ARG A 51 SHEET 5 AA 5 PHE A 248 GLU A 250 1 O GLU A 249 N TYR A 9 SHEET 1 AB 5 LEU A 16 LEU A 18 0 SHEET 2 AB 5 ARG A 25 ASN A 30 -1 O VAL A 29 N LEU A 17 SHEET 3 AB 5 LYS A 103 ALA A 112 -1 O ILE A 104 N LEU A 28 SHEET 4 AB 5 HIS A 56 SER A 63 -1 O GLY A 57 N PHE A 109 SHEET 5 AB 5 GLY A 73 ILE A 75 -1 O GLY A 73 N LEU A 60 SHEET 1 AC 4 LEU A 16 LEU A 18 0 SHEET 2 AC 4 ARG A 25 ASN A 30 -1 O VAL A 29 N LEU A 17 SHEET 3 AC 4 LYS A 103 ALA A 112 -1 O ILE A 104 N LEU A 28 SHEET 4 AC 4 ARG A 210 HIS A 218 -1 O TYR A 216 N ALA A 112 SHEET 1 AD 2 ILE A 34 LEU A 36 0 SHEET 2 AD 2 SER A 95 LEU A 97 -1 O SER A 95 N LEU A 36 SHEET 1 AE 2 LEU A 142 LEU A 144 0 SHEET 2 AE 2 VAL A 203 LEU A 205 -1 O VAL A 203 N LEU A 144 SHEET 1 AF 3 THR A 149 LEU A 154 0 SHEET 2 AF 3 VAL A 191 ASN A 197 -1 O VAL A 191 N LEU A 154 SHEET 3 AF 3 ILE A 179 VAL A 181 -1 O LEU A 180 N THR A 196 SHEET 1 AG 3 LEU A 222 THR A 223 0 SHEET 2 AG 3 LEU A 240 ARG A 242 -1 O LEU A 240 N THR A 223 SHEET 3 AG 3 SER A 230 ASP A 231 -1 O ASP A 231 N PHE A 241 SSBOND 1 CYS A 4 CYS A 246 1555 1555 2.03 LINK O2A DUT A1257 MG MG A1258 1555 1555 1.97 LINK O2B DUT A1257 MG MG A1258 1555 1555 2.10 LINK O2G DUT A1257 MG MG A1258 1555 1555 1.99 LINK MG MG A1258 O HOH A2046 1555 1555 2.13 LINK MG MG A1258 O HOH A2048 1555 1555 2.12 LINK MG MG A1258 O HOH A2082 1555 1555 2.17 SITE 1 AC1 21 LEU A 35 ARG A 37 HIS A 71 GLY A 73 SITE 2 AC1 21 ILE A 74 ASP A 76 TYR A 79 ARG A 84 SITE 3 AC1 21 ASN A 94 ARG A 171 SER A 172 GLY A 173 SITE 4 AC1 21 MG A1258 HOH A2046 HOH A2048 HOH A2078 SITE 5 AC1 21 HOH A2079 HOH A2080 HOH A2081 HOH A2082 SITE 6 AC1 21 HOH A2083 SITE 1 AC2 4 DUT A1257 HOH A2046 HOH A2048 HOH A2082 SITE 1 AC3 4 PRO A 162 HIS A 163 ARG A 165 LYS A 219 SITE 1 AC4 4 ARG A 171 ARG A 209 ARG A 210 HOH A2084 CRYST1 103.238 103.238 47.697 90.00 90.00 90.00 I 4 8 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 0.009686 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020966 0.00000