HEADER HYDROLASE 18-JAN-07 2OL0 TITLE HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DUTPASE, DUTP PYROPHOSPHATASE; COMPND 5 EC: 3.6.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VACCINIA VIRUS; SOURCE 3 ORGANISM_TAXID: 10245; SOURCE 4 GENE: DUT; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS FOLD, JELLY-ROLL, SUPERFAMILY, DUTPASE-LIKE, FORMS TIGHT TRIMER KEYWDS 2 THROUGH AN ADDITIONAL BETA-SHEET IN EACH SUBUNIT, SUBUNIT BETA- KEYWDS 3 SHEETS ARE ORTHOGONALLY PACKED AROUND THE THREE-FOLD AXIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.SCHORMANN,D.CHATTOPADHYAY REVDAT 5 30-AUG-23 2OL0 1 REMARK REVDAT 4 20-OCT-21 2OL0 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2OL0 1 VERSN REVDAT 2 24-FEB-09 2OL0 1 VERSN REVDAT 1 01-MAY-07 2OL0 0 JRNL AUTH A.SAMAL,N.SCHORMANN,W.J.COOK,L.J.DELUCAS,D.CHATTOPADHYAY JRNL TITL STRUCTURES OF VACCINIA VIRUS DUTPASE AND ITS NUCLEOTIDE JRNL TITL 2 COMPLEXES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 63 571 2007 JRNL REFN ISSN 0907-4449 JRNL PMID 17452782 JRNL DOI 10.1107/S0907444907007871 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.3.0011 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22718 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1156 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1653 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2915 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.255 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.539 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3092 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4184 ; 1.188 ; 2.015 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 370 ; 5.967 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;30.469 ;23.262 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 525 ;14.437 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;21.186 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 442 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2346 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1279 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2058 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 250 ; 0.138 ; 0.200 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): 28 ; 0.151 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.181 ; 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): 1904 ; 0.348 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3004 ; 0.599 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1348 ; 1.022 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1180 ; 1.698 ; 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 : 3 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 8 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): -20.641 -28.0630 6.7980 REMARK 3 T TENSOR REMARK 3 T11: -0.1205 T22: -0.0848 REMARK 3 T33: -0.0206 T12: 0.0003 REMARK 3 T13: -0.0187 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.2603 L22: 1.1212 REMARK 3 L33: 2.8215 L12: -0.1243 REMARK 3 L13: 0.1980 L23: 0.4610 REMARK 3 S TENSOR REMARK 3 S11: -0.0131 S12: 0.0171 S13: -0.0041 REMARK 3 S21: -0.1260 S22: 0.0894 S23: -0.1430 REMARK 3 S31: 0.2480 S32: 0.0287 S33: 0.2411 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 131 REMARK 3 ORIGIN FOR THE GROUP (A): -40.102 -26.0770 4.5840 REMARK 3 T TENSOR REMARK 3 T11: -0.1189 T22: -0.0963 REMARK 3 T33: -0.0154 T12: 0.0067 REMARK 3 T13: 0.0208 T23: -0.0276 REMARK 3 L TENSOR REMARK 3 L11: 2.2751 L22: 2.3926 REMARK 3 L33: 2.1257 L12: -0.5940 REMARK 3 L13: 0.5094 L23: 0.2206 REMARK 3 S TENSOR REMARK 3 S11: -0.0143 S12: -0.0456 S13: 0.0598 REMARK 3 S21: -0.1559 S22: -0.0245 S23: 0.3621 REMARK 3 S31: -0.0394 S32: 0.0654 S33: -0.2256 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 7 C 131 REMARK 3 ORIGIN FOR THE GROUP (A): -29.464 -34.3690 -9.7670 REMARK 3 T TENSOR REMARK 3 T11: -0.0804 T22: -0.1157 REMARK 3 T33: -0.0629 T12: 0.0124 REMARK 3 T13: -0.0089 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 1.3836 L22: 1.8783 REMARK 3 L33: 2.8384 L12: -0.6743 REMARK 3 L13: -0.2384 L23: 0.5606 REMARK 3 S TENSOR REMARK 3 S11: 0.0237 S12: -0.0290 S13: 0.0052 REMARK 3 S21: 0.0103 S22: -0.1078 S23: 0.0738 REMARK 3 S31: -0.1479 S32: -0.0161 S33: 0.0943 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 2OL0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041267. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24014 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 19.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : 0.07800 REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : 0.34700 REMARK 200 FOR SHELL : 3.400 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 2OKD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG2000 MME, 0.1M TRIS, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.44000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.72000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.08000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 8.36000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.80000 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS A HOMO-TRIMER WITH MONOMERS REMARK 300 RELATED BY NON-CRYSTALLOGRAPHIC SYMMETRY. THIS HOMO-TRIMER REMARK 300 CONSTITUTES THE BIOLOGICAL ASSEMBLY. 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: 11060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 MET A 1 REMARK 465 PHE A 2 REMARK 465 ASN A 3 REMARK 465 MET A 4 REMARK 465 ASN A 5 REMARK 465 ILE A 6 REMARK 465 ASN A 7 REMARK 465 ASP A 132 REMARK 465 SER A 133 REMARK 465 THR A 134 REMARK 465 ASN A 135 REMARK 465 ARG A 136 REMARK 465 GLY A 137 REMARK 465 ASP A 138 REMARK 465 GLN A 139 REMARK 465 GLY A 140 REMARK 465 PHE A 141 REMARK 465 GLY A 142 REMARK 465 SER A 143 REMARK 465 THR A 144 REMARK 465 GLY A 145 REMARK 465 LEU A 146 REMARK 465 ARG A 147 REMARK 465 MET B 1 REMARK 465 PHE B 2 REMARK 465 ASN B 3 REMARK 465 MET B 4 REMARK 465 ASN B 5 REMARK 465 ILE B 6 REMARK 465 ASN B 7 REMARK 465 ASP B 132 REMARK 465 SER B 133 REMARK 465 THR B 134 REMARK 465 ASN B 135 REMARK 465 ARG B 136 REMARK 465 GLY B 137 REMARK 465 ASP B 138 REMARK 465 GLN B 139 REMARK 465 GLY B 140 REMARK 465 PHE B 141 REMARK 465 GLY B 142 REMARK 465 SER B 143 REMARK 465 THR B 144 REMARK 465 GLY B 145 REMARK 465 LEU B 146 REMARK 465 ARG B 147 REMARK 465 MET C 1 REMARK 465 PHE C 2 REMARK 465 ASN C 3 REMARK 465 MET C 4 REMARK 465 ASN C 5 REMARK 465 ILE C 6 REMARK 465 ASP C 132 REMARK 465 SER C 133 REMARK 465 THR C 134 REMARK 465 ASN C 135 REMARK 465 ARG C 136 REMARK 465 GLY C 137 REMARK 465 ASP C 138 REMARK 465 GLN C 139 REMARK 465 GLY C 140 REMARK 465 PHE C 141 REMARK 465 GLY C 142 REMARK 465 SER C 143 REMARK 465 THR C 144 REMARK 465 GLY C 145 REMARK 465 LEU C 146 REMARK 465 ARG C 147 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 GLN C 129 CD GLN C 129 OE1 0.154 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 B 122 73.69 -119.66 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 B 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 25 OE1 REMARK 620 2 HOH B1233 O 87.1 REMARK 620 3 HOH B1269 O 77.5 155.2 REMARK 620 4 DUD C1203 O2A 147.3 72.8 129.1 REMARK 620 5 DUD C1203 O1B 104.3 124.8 78.3 69.5 REMARK 620 6 HOH C1229 O 89.8 84.7 76.1 112.9 147.2 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 CL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUD C 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUD B 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DUD C 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OKD RELATED DB: PDB REMARK 900 APO-ENZYME OF VACCINIA VIRUS DUTPASE REMARK 900 RELATED ID: 2OKB RELATED DB: PDB REMARK 900 N-TERMINALLY TRUNCATED VERSION OF VACCINIA VIRUS DUTPASE REMARK 900 RELATED ID: 2OKE RELATED DB: PDB REMARK 900 STRUCTURE OF VACCINIA VIRUS DUTPASE WITH SUBSTRATE ANALOG REMARK 900 RELATED ID: 2OL1 RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURES OF VACCINIA VIRUS DUTPASE DBREF 2OL0 A 1 147 GB 29692147 AAO89320 1 147 DBREF 2OL0 B 1 147 GB 29692147 AAO89320 1 147 DBREF 2OL0 C 1 147 GB 29692147 AAO89320 1 147 SEQADV 2OL0 GLY A 28 GB 29692147 TYR 28 ENGINEERED MUTATION SEQADV 2OL0 GLY B 28 GB 29692147 TYR 28 ENGINEERED MUTATION SEQADV 2OL0 GLY C 28 GB 29692147 TYR 28 ENGINEERED MUTATION SEQRES 1 A 147 MET PHE ASN MET ASN ILE ASN SER PRO VAL ARG PHE VAL SEQRES 2 A 147 LYS GLU THR ASN ARG ALA LYS SER PRO THR ARG GLN SER SEQRES 3 A 147 PRO GLY ALA ALA GLY TYR ASP LEU TYR SER ALA TYR ASP SEQRES 4 A 147 TYR THR ILE PRO PRO GLY GLU ARG GLN LEU ILE LYS THR SEQRES 5 A 147 ASP ILE SER MET SER MET PRO LYS PHE CYS TYR GLY ARG SEQRES 6 A 147 ILE ALA PRO ARG SER GLY LEU SER LEU LYS GLY ILE ASP SEQRES 7 A 147 ILE GLY GLY GLY VAL ILE ASP GLU ASP TYR ARG GLY ASN SEQRES 8 A 147 ILE GLY VAL ILE LEU ILE ASN ASN GLY LYS CYS THR PHE SEQRES 9 A 147 ASN VAL ASN THR GLY ASP ARG ILE ALA GLN LEU ILE TYR SEQRES 10 A 147 GLN ARG ILE TYR TYR PRO GLU LEU GLU GLU VAL GLN SER SEQRES 11 A 147 LEU ASP SER THR ASN ARG GLY ASP GLN GLY PHE GLY SER SEQRES 12 A 147 THR GLY LEU ARG SEQRES 1 B 147 MET PHE ASN MET ASN ILE ASN SER PRO VAL ARG PHE VAL SEQRES 2 B 147 LYS GLU THR ASN ARG ALA LYS SER PRO THR ARG GLN SER SEQRES 3 B 147 PRO GLY ALA ALA GLY TYR ASP LEU TYR SER ALA TYR ASP SEQRES 4 B 147 TYR THR ILE PRO PRO GLY GLU ARG GLN LEU ILE LYS THR SEQRES 5 B 147 ASP ILE SER MET SER MET PRO LYS PHE CYS TYR GLY ARG SEQRES 6 B 147 ILE ALA PRO ARG SER GLY LEU SER LEU LYS GLY ILE ASP SEQRES 7 B 147 ILE GLY GLY GLY VAL ILE ASP GLU ASP TYR ARG GLY ASN SEQRES 8 B 147 ILE GLY VAL ILE LEU ILE ASN ASN GLY LYS CYS THR PHE SEQRES 9 B 147 ASN VAL ASN THR GLY ASP ARG ILE ALA GLN LEU ILE TYR SEQRES 10 B 147 GLN ARG ILE TYR TYR PRO GLU LEU GLU GLU VAL GLN SER SEQRES 11 B 147 LEU ASP SER THR ASN ARG GLY ASP GLN GLY PHE GLY SER SEQRES 12 B 147 THR GLY LEU ARG SEQRES 1 C 147 MET PHE ASN MET ASN ILE ASN SER PRO VAL ARG PHE VAL SEQRES 2 C 147 LYS GLU THR ASN ARG ALA LYS SER PRO THR ARG GLN SER SEQRES 3 C 147 PRO GLY ALA ALA GLY TYR ASP LEU TYR SER ALA TYR ASP SEQRES 4 C 147 TYR THR ILE PRO PRO GLY GLU ARG GLN LEU ILE LYS THR SEQRES 5 C 147 ASP ILE SER MET SER MET PRO LYS PHE CYS TYR GLY ARG SEQRES 6 C 147 ILE ALA PRO ARG SER GLY LEU SER LEU LYS GLY ILE ASP SEQRES 7 C 147 ILE GLY GLY GLY VAL ILE ASP GLU ASP TYR ARG GLY ASN SEQRES 8 C 147 ILE GLY VAL ILE LEU ILE ASN ASN GLY LYS CYS THR PHE SEQRES 9 C 147 ASN VAL ASN THR GLY ASP ARG ILE ALA GLN LEU ILE TYR SEQRES 10 C 147 GLN ARG ILE TYR TYR PRO GLU LEU GLU GLU VAL GLN SER SEQRES 11 C 147 LEU ASP SER THR ASN ARG GLY ASP GLN GLY PHE GLY SER SEQRES 12 C 147 THR GLY LEU ARG HET CL A 300 1 HET MG B 500 1 HET DUD B1202 24 HET EDO B 403 4 HET DUD C1201 24 HET DUD C1203 24 HET EDO C 401 4 HET EDO C 402 4 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM DUD DEOXYURIDINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 CL CL 1- FORMUL 5 MG MG 2+ FORMUL 6 DUD 3(C9 H14 N2 O11 P2) FORMUL 7 EDO 3(C2 H6 O2) FORMUL 12 HOH *206(H2 O) HELIX 1 1 ARG A 69 LYS A 75 1 7 HELIX 2 2 ARG B 69 LYS B 75 1 7 HELIX 3 3 ARG C 69 LYS C 75 1 7 SHEET 1 A 3 ILE A 54 SER A 57 0 SHEET 2 A 3 VAL A 10 LYS A 14 -1 N VAL A 13 O SER A 55 SHEET 3 A 3 LEU B 125 GLU B 127 1 O GLU B 126 N VAL A 10 SHEET 1 B 6 TYR A 32 TYR A 35 0 SHEET 2 B 6 ARG A 111 TYR A 121 -1 O LEU A 115 N TYR A 32 SHEET 3 B 6 CYS A 62 ALA A 67 -1 N ARG A 65 O ILE A 116 SHEET 4 B 6 VAL A 83 ILE A 84 -1 O ILE A 84 N GLY A 64 SHEET 5 B 6 CYS A 62 ALA A 67 -1 N GLY A 64 O ILE A 84 SHEET 6 B 6 ARG A 111 TYR A 121 -1 O ILE A 116 N ARG A 65 SHEET 1 C 7 ARG C 111 TYR C 121 0 SHEET 2 C 7 ARG B 111 TYR B 121 -1 N TYR B 117 O TYR C 121 SHEET 3 C 7 TYR B 32 TYR B 35 -1 N TYR B 32 O LEU B 115 SHEET 4 C 7 ARG B 111 TYR B 121 -1 O LEU B 115 N TYR B 32 SHEET 5 C 7 CYS B 62 ALA B 67 -1 N ALA B 67 O GLN B 114 SHEET 6 C 7 VAL B 83 ILE B 84 -1 O ILE B 84 N GLY B 64 SHEET 7 C 7 CYS B 62 ALA B 67 -1 N GLY B 64 O ILE B 84 SHEET 1 D 9 ARG B 111 TYR B 121 0 SHEET 2 D 9 ARG A 111 TYR A 121 -1 N TYR A 117 O TYR B 121 SHEET 3 D 9 ARG C 111 TYR C 121 -1 O TYR C 117 N TYR A 121 SHEET 4 D 9 TYR C 32 TYR C 35 -1 N TYR C 32 O LEU C 115 SHEET 5 D 9 ARG C 111 TYR C 121 -1 O LEU C 115 N TYR C 32 SHEET 6 D 9 CYS C 62 ALA C 67 -1 N ARG C 65 O ILE C 116 SHEET 7 D 9 VAL C 83 ILE C 84 -1 O ILE C 84 N GLY C 64 SHEET 8 D 9 CYS C 62 ALA C 67 -1 N GLY C 64 O ILE C 84 SHEET 9 D 9 ARG C 111 TYR C 121 -1 O ILE C 116 N ARG C 65 SHEET 1 E 2 TYR A 40 ILE A 42 0 SHEET 2 E 2 PHE A 104 VAL A 106 -1 O VAL A 106 N TYR A 40 SHEET 1 F 3 ARG A 47 LYS A 51 0 SHEET 2 F 3 GLY A 93 ASN A 98 -1 O VAL A 94 N ILE A 50 SHEET 3 F 3 ILE A 77 GLY A 80 -1 N ASP A 78 O ILE A 97 SHEET 1 G 3 LEU A 125 GLU A 127 0 SHEET 2 G 3 VAL C 10 LYS C 14 1 O VAL C 10 N GLU A 126 SHEET 3 G 3 ILE C 54 SER C 57 -1 O SER C 55 N VAL C 13 SHEET 1 H 3 ILE B 54 SER B 57 0 SHEET 2 H 3 VAL B 10 LYS B 14 -1 N VAL B 13 O SER B 55 SHEET 3 H 3 LEU C 125 GLU C 127 1 O GLU C 126 N VAL B 10 SHEET 1 I 2 TYR B 40 ILE B 42 0 SHEET 2 I 2 PHE B 104 VAL B 106 -1 O PHE B 104 N ILE B 42 SHEET 1 J 3 GLU B 46 LYS B 51 0 SHEET 2 J 3 GLY B 93 ASN B 98 -1 O VAL B 94 N ILE B 50 SHEET 3 J 3 ILE B 77 GLY B 80 -1 N ASP B 78 O ILE B 97 SHEET 1 K 2 TYR C 40 ILE C 42 0 SHEET 2 K 2 PHE C 104 VAL C 106 -1 O VAL C 106 N TYR C 40 SHEET 1 L 3 ARG C 47 LYS C 51 0 SHEET 2 L 3 GLY C 93 ASN C 98 -1 O VAL C 94 N ILE C 50 SHEET 3 L 3 ILE C 77 GLY C 80 -1 N ASP C 78 O ILE C 97 LINK OE1 GLN B 25 MG MG B 500 1555 1555 2.98 LINK MG MG B 500 O HOH B1233 1555 1555 3.01 LINK MG MG B 500 O HOH B1269 1555 1555 3.13 LINK MG MG B 500 O2A DUD C1203 1555 1555 2.63 LINK MG MG B 500 O1B DUD C1203 1555 1555 2.31 LINK MG MG B 500 O HOH C1229 1555 1555 2.77 SITE 1 AC1 5 GLN A 118 ARG B 65 GLN B 118 TYR C 63 SITE 2 AC1 5 GLN C 118 SITE 1 AC2 4 GLN B 25 HOH B1233 DUD C1203 HOH C1229 SITE 1 AC3 12 GLY A 82 VAL A 83 ILE A 84 ASP A 85 SITE 2 AC3 12 TYR A 88 GLY A 93 ARG C 69 SER C 70 SITE 3 AC3 12 GLY C 71 ARG C 111 HOH C1207 HOH C1276 SITE 1 AC4 13 ARG A 69 SER A 70 GLY A 71 ARG A 111 SITE 2 AC4 13 HOH A 360 GLY B 82 VAL B 83 ILE B 84 SITE 3 AC4 13 ASP B 85 TYR B 88 GLY B 93 ILE B 95 SITE 4 AC4 13 HOH B1203 SITE 1 AC5 16 ARG B 69 SER B 70 GLY B 71 EDO B 403 SITE 2 AC5 16 MG B 500 GLY C 82 VAL C 83 ILE C 84 SITE 3 AC5 16 ASP C 85 TYR C 88 GLY C 93 ILE C 95 SITE 4 AC5 16 EDO C 401 HOH C1208 HOH C1242 HOH C1269 SITE 1 AC6 5 SER B 26 ASP C 85 ASP C 87 TYR C 88 SITE 2 AC6 5 DUD C1203 SITE 1 AC7 6 GLN A 118 ARG A 119 GLN B 118 ARG B 119 SITE 2 AC7 6 GLN C 118 ARG C 119 SITE 1 AC8 6 SER B 70 HOH B1251 HOH B1255 LEU C 49 SITE 2 AC8 6 GLY C 93 DUD C1203 CRYST1 119.660 119.660 50.160 90.00 90.00 120.00 P 65 18 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 0.008357 0.004825 0.000000 0.00000 SCALE2 0.000000 0.009650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019936 0.00000