PDB Short entry for 1V7R HEADER HYDROLASE 22-DEC-03 1V7R TITLE STRUCTURE OF NUCLEOTIDE TRIPHOSPHATE PYROPHOSPHATASE FROM PYROCOCCUS TITLE 2 HORIKOSHII OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PH1917; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEOTIDE TRIPHOSPHATE PYROPHOSPHATASE; COMPND 5 EC: 3.6.1.19; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 GENE: NTPASE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS NTPASE, STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, RSGI, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.K.LOKANATH,N.KUNISHIMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 6 25-OCT-23 1V7R 1 REMARK REVDAT 5 13-JUL-11 1V7R 1 VERSN REVDAT 4 09-JUN-09 1V7R 1 REVDAT REVDAT 3 24-FEB-09 1V7R 1 VERSN REVDAT 2 27-JAN-09 1V7R 1 JRNL REVDAT 1 30-DEC-03 1V7R 0 JRNL AUTH N.K.LOKANATH,K.J.PAMPA,K.TAKIO,N.KUNISHIMA JRNL TITL STRUCTURES OF DIMERIC NONSTANDARD NUCLEOTIDE TRIPHOSPHATE JRNL TITL 2 PYROPHOSPHATASE FROM PYROCOCCUS HORIKOSHII OT3: FUNCTIONAL JRNL TITL 3 SIGNIFICANCE OF INTERPROTOMER CONFORMATIONAL CHANGES. JRNL REF J.MOL.BIOL. V. 375 1013 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18062990 JRNL DOI 10.1016/J.JMB.2007.11.018 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1374304.660 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 40654 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 SET) : 0.202 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2038 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6361 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 202 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : -5.58000 REMARK 3 B33 (A**2) : 4.87000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.09 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.660 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.760 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 42.46 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CIT.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CIT.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1V7R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000006312. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40654 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1B78 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M TRIS SODIUM CITRATE, PH 5.1, REMARK 280 MICROBATCH, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 27.81050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.81050 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.50650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.59400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.50650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.59400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 27.81050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.50650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.59400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 27.81050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.50650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.59400 REMARK 290 SMTRY3 8 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 39.50650 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 139.78200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 27.81050 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 1256 O HOH A 1389 2.18 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 THR A 87 -70.80 -95.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 1200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PHO001001917.1 RELATED DB: TARGETDB DBREF 1V7R A 1 186 UNP O59580 O59580_PYRHO 1 186 SEQRES 1 A 186 MET LYS ILE PHE PHE ILE THR SER ASN PRO GLY LYS VAL SEQRES 2 A 186 ARG GLU VAL ALA ASN PHE LEU GLY THR PHE GLY ILE GLU SEQRES 3 A 186 ILE VAL GLN LEU LYS HIS GLU TYR PRO GLU ILE GLN ALA SEQRES 4 A 186 GLU LYS LEU GLU ASP VAL VAL ASP PHE GLY ILE SER TRP SEQRES 5 A 186 LEU LYS GLY LYS VAL PRO GLU PRO PHE MET ILE GLU ASP SEQRES 6 A 186 SER GLY LEU PHE ILE GLU SER LEU LYS GLY PHE PRO GLY SEQRES 7 A 186 VAL TYR SER SER TYR VAL TYR ARG THR ILE GLY LEU GLU SEQRES 8 A 186 GLY ILE LEU LYS LEU MET GLU GLY ALA GLU ASP ARG ARG SEQRES 9 A 186 ALA TYR PHE LYS SER VAL ILE GLY PHE TYR ILE ASP GLY SEQRES 10 A 186 LYS ALA TYR LYS PHE SER GLY VAL THR TRP GLY ARG ILE SEQRES 11 A 186 SER ASN GLU LYS ARG GLY THR HIS GLY PHE GLY TYR ASP SEQRES 12 A 186 PRO ILE PHE ILE PRO GLU GLY SER GLU LYS THR PHE ALA SEQRES 13 A 186 GLU MET THR ILE GLU GLU LYS ASN ALA LEU SER HIS ARG SEQRES 14 A 186 GLY LYS ALA LEU LYS ALA PHE PHE GLU TRP LEU LYS VAL SEQRES 15 A 186 ASN LEU LYS TYR HET CIT A1200 13 HETNAM CIT CITRIC ACID FORMUL 2 CIT C6 H8 O7 FORMUL 3 HOH *202(H2 O) HELIX 1 1 ASN A 9 THR A 22 1 14 HELIX 2 2 LYS A 41 LYS A 54 1 14 HELIX 3 3 SER A 72 LYS A 74 5 3 HELIX 4 4 PRO A 77 VAL A 79 5 3 HELIX 5 5 TYR A 80 ILE A 88 1 9 HELIX 6 6 ILE A 88 MET A 97 1 10 HELIX 7 7 TYR A 142 PRO A 144 5 3 HELIX 8 8 THR A 154 MET A 158 5 5 HELIX 9 9 THR A 159 ALA A 165 1 7 HELIX 10 10 SER A 167 LYS A 185 1 19 SHEET 1 A 6 GLU A 26 LEU A 30 0 SHEET 2 A 6 LYS A 2 ILE A 6 1 N ILE A 3 O GLU A 26 SHEET 3 A 6 PHE A 61 ILE A 70 1 O MET A 62 N PHE A 4 SHEET 4 A 6 ARG A 104 ILE A 115 -1 O TYR A 106 N PHE A 69 SHEET 5 A 6 LYS A 118 ILE A 130 -1 O PHE A 122 N ILE A 111 SHEET 6 A 6 PHE A 146 PRO A 148 -1 O ILE A 147 N ARG A 129 CISPEP 1 GLU A 59 PRO A 60 0 -0.11 CISPEP 2 PHE A 76 PRO A 77 0 0.48 SITE 1 AC1 15 TYR A 106 LYS A 108 VAL A 125 TRP A 127 SITE 2 AC1 15 HIS A 138 THR A 159 ILE A 160 HOH A1217 SITE 3 AC1 15 HOH A1268 HOH A1281 HOH A1300 HOH A1314 SITE 4 AC1 15 HOH A1322 HOH A1357 HOH A1366 CRYST1 79.013 93.188 55.621 90.00 90.00 90.00 C 2 2 21 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 0.012656 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010731 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017979 0.00000