PDB Short entry for 1WR2 HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 08-OCT-04 1WR2 TITLE CRYSTAL STRUCTURE OF PH1788 FROM PYROCOCCUS HORIKOSHII OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PH1789; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS PYROCOCCUS HORIKOSHII, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT KEYWDS 2 ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR M.SUGAHARA,N.KUNISHIMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 4 13-MAR-24 1WR2 1 REMARK REVDAT 3 13-JUL-11 1WR2 1 VERSN REVDAT 2 24-FEB-09 1WR2 1 VERSN REVDAT 1 18-OCT-05 1WR2 0 JRNL AUTH M.SUGAHARA,N.KUNISHIMA JRNL TITL CRYSTAL STRUCTURE OF PH1788 FROM PYROCOCCUS HORIKOSHII OT3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18886 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) : 0.228 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 923 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 86 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1861 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.97000 REMARK 3 B22 (A**2) : -4.55000 REMARK 3 B33 (A**2) : 0.58000 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) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1WR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000023899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-04; 04-OCT-04; 02-OCT-04 REMARK 200 TEMPERATURE (KELVIN) : 100; 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : SPRING-8; SPRING-8; SPRING-8 REMARK 200 BEAMLINE : BL26B1; BL26B1; BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000; 1.07172; 1.0080 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V; RIGAKU JUPITER; REMARK 200 RIGAKU JUPITER REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18934 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6000 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.70200 REMARK 200 R SYM FOR SHELL (I) : 0.64700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: JAM, PH 6.5, MICROBATCH, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.17300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.06700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.32150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.06700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.17300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.32150 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: MONOMERIC 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 ARG A 180 REMARK 465 GLY A 181 REMARK 465 ASP A 238 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 ASN A 80 52.80 37.60 REMARK 500 ASN A 214 117.13 -161.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: PHO001001788.1 RELATED DB: TARGETDB DBREF 1WR2 A 1 238 UNP O59452 O59452_PYRHO 1 238 SEQRES 1 A 238 MET LYS GLU GLU ALA VAL ARG VAL ILE GLU GLU VAL LEU SEQRES 2 A 238 LYS GLN GLY ARG THR ALA MET VAL GLU TYR GLU ALA LYS SEQRES 3 A 238 GLN VAL LEU LYS ALA TYR GLY LEU PRO VAL PRO GLU GLU SEQRES 4 A 238 LYS LEU ALA LYS THR LEU ASP GLU ALA LEU GLU TYR ALA SEQRES 5 A 238 LYS GLU ILE GLY TYR PRO VAL VAL LEU LYS LEU MET SER SEQRES 6 A 238 PRO GLN ILE LEU HIS LYS SER ASP ALA LYS VAL VAL MET SEQRES 7 A 238 LEU ASN ILE LYS ASN GLU GLU GLU LEU LYS LYS LYS TRP SEQRES 8 A 238 GLU GLU ILE HIS GLU ASN ALA LYS LYS TYR ARG PRO ASP SEQRES 9 A 238 ALA GLU ILE LEU GLY VAL LEU VAL ALA PRO MET LEU LYS SEQRES 10 A 238 PRO GLY ARG GLU VAL ILE ILE GLY VAL THR GLU ASP PRO SEQRES 11 A 238 GLN PHE GLY HIS ALA ILE MET PHE GLY LEU GLY GLY ILE SEQRES 12 A 238 PHE VAL GLU ILE LEU LYS ASP VAL THR PHE ARG LEU VAL SEQRES 13 A 238 PRO ILE THR GLU LYS ASP ALA ARG LYS MET ILE GLN GLU SEQRES 14 A 238 ILE LYS ALA TYR PRO ILE LEU ALA GLY ALA ARG GLY GLU SEQRES 15 A 238 GLU PRO ALA ASP ILE ASP ALA ILE VAL ASP MET LEU LEU SEQRES 16 A 238 LYS VAL SER LYS LEU VAL ASP ASP LEU LYS ASP TYR ILE SEQRES 17 A 238 LYS GLU MET ASP LEU ASN PRO VAL PHE VAL TYR ASN LYS SEQRES 18 A 238 GLY GLU GLY ALA VAL ILE VAL ASP SER ARG ILE ILE LEU SEQRES 19 A 238 LYS PRO LYS ASP FORMUL 2 HOH *175(H2 O) HELIX 1 1 LYS A 2 GLN A 15 1 14 HELIX 2 2 VAL A 21 ALA A 31 1 11 HELIX 3 3 THR A 44 GLY A 56 1 13 HELIX 4 4 HIS A 70 LYS A 75 1 6 HELIX 5 5 ASN A 83 ARG A 102 1 20 HELIX 6 6 PHE A 144 LYS A 149 1 6 HELIX 7 7 THR A 159 GLU A 169 1 11 HELIX 8 8 ALA A 172 GLY A 178 1 7 HELIX 9 9 ASP A 186 LEU A 204 1 19 SHEET 1 A 6 ALA A 19 MET A 20 0 SHEET 2 A 6 SER A 230 LEU A 234 -1 O ILE A 232 N MET A 20 SHEET 3 A 6 ILE A 208 VAL A 218 -1 N GLU A 210 O ILE A 233 SHEET 4 A 6 ARG A 120 ASP A 129 -1 N VAL A 126 O MET A 211 SHEET 5 A 6 GLY A 133 LEU A 140 -1 O GLY A 133 N ASP A 129 SHEET 6 A 6 THR A 152 LEU A 155 -1 O ARG A 154 N ILE A 136 SHEET 1 B 4 ALA A 19 MET A 20 0 SHEET 2 B 4 SER A 230 LEU A 234 -1 O ILE A 232 N MET A 20 SHEET 3 B 4 ILE A 208 VAL A 218 -1 N GLU A 210 O ILE A 233 SHEET 4 B 4 ALA A 225 ILE A 227 -1 O VAL A 226 N PHE A 217 SHEET 1 C 4 LYS A 40 ALA A 42 0 SHEET 2 C 4 GLY A 109 PRO A 114 -1 O VAL A 112 N LYS A 40 SHEET 3 C 4 VAL A 59 MET A 64 -1 N LYS A 62 O LEU A 111 SHEET 4 C 4 VAL A 77 ILE A 81 -1 O ILE A 81 N VAL A 59 CISPEP 1 TYR A 57 PRO A 58 0 -0.04 CISPEP 2 VAL A 156 PRO A 157 0 0.08 CISPEP 3 ASN A 214 PRO A 215 0 0.20 CRYST1 46.346 60.643 96.134 90.00 90.00 90.00 P 21 21 21 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 0.021577 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016490 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010402 0.00000