HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 28-DEC-04 1YE5 TITLE CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN OF UNKNOWN FUNCTION FROM TITLE 2 PYROCOCCUS HORIKOSHII OT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PH0500; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-CODON PLUS (DE3)-RIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-11A KEYWDS ROSSMANN FOLD, TRNA SYNTHETASE, NUCLEOTIDE BINDING PROTEIN, PIN KEYWDS 2 DOMAIN, STRUCTURAL GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.JEYAKANTHAN,T.H.TAHIROV,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 25-OCT-23 1YE5 1 REMARK REVDAT 2 24-FEB-09 1YE5 1 VERSN REVDAT 1 17-MAY-05 1YE5 0 JRNL AUTH J.JEYAKANTHAN,E.INAGAKI,C.KUROISHI,T.H.TAHIROV JRNL TITL STRUCTURE OF PIN-DOMAIN PROTEIN PH0500 FROM PYROCOCCUS JRNL TITL 2 HORIKOSHII. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 61 463 2005 JRNL REFN ESSN 1744-3091 JRNL PMID 16511069 JRNL DOI 10.1107/S1744309105012406 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) : 19.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 926739.160 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 18036 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) : 0.234 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1231 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2450 REMARK 3 BIN R VALUE (WORKING SET) : 0.4070 REMARK 3 BIN FREE R VALUE : 0.4440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 193 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2335 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.33 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 61.01 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 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 : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18805 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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 (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: AMORE REMARK 200 STARTING MODEL: 1V96 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% PEG 4000, 0.1M MES BUFFER, PH REMARK 280 5.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.19050 REMARK 290 SMTRY3 2 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 300 REMARK: THE CRYSTALLOGRAPHY ASYMMETRIC UNIT WHICH CONSISTS OF TWO REMARK 300 CHAINS (A AND B). BIOLOGICAL UNITS IS A HOMODIMER 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 VAL A 144 REMARK 465 GLU A 145 REMARK 465 LYS A 146 REMARK 465 GLU A 147 REMARK 465 LEU A 148 REMARK 465 ILE A 149 REMARK 465 MET B 1 REMARK 465 ILE B 149 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 MET A 143 CG SD CE 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 GLU A 141 85.46 -68.93 REMARK 500 LEU A 142 149.98 149.39 REMARK 500 LEU B 52 34.69 -93.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1V96 RELATED DB: PDB REMARK 900 SPACE GROUP IS DIFFERENT REMARK 900 RELATED ID: PHO001000500 RELATED DB: TARGETDB DBREF 1YE5 A 1 149 UNP O58236 O58236_PYRHO 1 149 DBREF 1YE5 B 1 149 UNP O58236 O58236_PYRHO 1 149 SEQRES 1 A 149 MET PRO LEU PRO PRO ASP ILE THR PHE ASP SER LEU ALA SEQRES 2 A 149 LEU ILE LYS MET HIS SER GLN ASN MET LYS ARG ILE LEU SEQRES 3 A 149 GLU VAL THR LEU ALA LYS PHE THR VAL ASN LEU SER ILE SEQRES 4 A 149 VAL THR VAL TYR ARG TYR LEU THR ALA ARG ALA TYR LEU SEQRES 5 A 149 LYS LYS ASN ILE GLU ALA GLU PHE GLU ILE LEU LYS ASP SEQRES 6 A 149 ILE TYR ASN ILE VAL PRO LEU LEU ASP ASP ILE ALA ILE SEQRES 7 A 149 LYS ALA ALA GLN ILE GLU ALA ASN LEU ILE LYS LYS GLU SEQRES 8 A 149 ILE THR LEU ASP MET GLU ASP ILE ILE THR ALA THR THR SEQRES 9 A 149 ALA ILE TYR THR ASN SER LEU LEU VAL THR ASP ASP PRO SEQRES 10 A 149 LYS ARG TYR GLU PRO ILE ARG ARG PHE GLY LEU ASP THR SEQRES 11 A 149 MET PRO LEU ASP LYS PHE ILE LYS GLU VAL GLU LEU MET SEQRES 12 A 149 VAL GLU LYS GLU LEU ILE SEQRES 1 B 149 MET PRO LEU PRO PRO ASP ILE THR PHE ASP SER LEU ALA SEQRES 2 B 149 LEU ILE LYS MET HIS SER GLN ASN MET LYS ARG ILE LEU SEQRES 3 B 149 GLU VAL THR LEU ALA LYS PHE THR VAL ASN LEU SER ILE SEQRES 4 B 149 VAL THR VAL TYR ARG TYR LEU THR ALA ARG ALA TYR LEU SEQRES 5 B 149 LYS LYS ASN ILE GLU ALA GLU PHE GLU ILE LEU LYS ASP SEQRES 6 B 149 ILE TYR ASN ILE VAL PRO LEU LEU ASP ASP ILE ALA ILE SEQRES 7 B 149 LYS ALA ALA GLN ILE GLU ALA ASN LEU ILE LYS LYS GLU SEQRES 8 B 149 ILE THR LEU ASP MET GLU ASP ILE ILE THR ALA THR THR SEQRES 9 B 149 ALA ILE TYR THR ASN SER LEU LEU VAL THR ASP ASP PRO SEQRES 10 B 149 LYS ARG TYR GLU PRO ILE ARG ARG PHE GLY LEU ASP THR SEQRES 11 B 149 MET PRO LEU ASP LYS PHE ILE LYS GLU VAL GLU LEU MET SEQRES 12 B 149 VAL GLU LYS GLU LEU ILE FORMUL 3 HOH *217(H2 O) HELIX 1 1 ASP A 10 HIS A 18 1 9 HELIX 2 2 SER A 19 ASN A 21 5 3 HELIX 3 3 MET A 22 PHE A 33 1 12 HELIX 4 4 ILE A 39 ARG A 49 1 11 HELIX 5 5 ASN A 55 TYR A 67 1 13 HELIX 6 6 LEU A 73 LYS A 90 1 18 HELIX 7 7 ASP A 95 ASN A 109 1 15 HELIX 8 8 ASP A 116 GLU A 121 1 6 HELIX 9 9 PRO A 122 GLY A 127 5 6 HELIX 10 10 LEU A 133 GLU A 141 1 9 HELIX 11 11 ASP B 10 HIS B 18 1 9 HELIX 12 12 SER B 19 ASN B 21 5 3 HELIX 13 13 MET B 22 PHE B 33 1 12 HELIX 14 14 ILE B 39 LEU B 52 1 14 HELIX 15 15 ASN B 55 ASP B 65 1 11 HELIX 16 16 LEU B 73 LYS B 89 1 17 HELIX 17 17 ASP B 95 ASN B 109 1 15 HELIX 18 18 ASP B 116 GLY B 127 5 12 HELIX 19 19 LEU B 133 GLU B 147 1 15 SHEET 1 A 5 ASN A 68 VAL A 70 0 SHEET 2 A 5 THR A 34 SER A 38 1 N LEU A 37 O VAL A 70 SHEET 3 A 5 ASP A 6 PHE A 9 1 N ILE A 7 O THR A 34 SHEET 4 A 5 LEU A 111 THR A 114 1 O VAL A 113 N THR A 8 SHEET 5 A 5 THR A 130 PRO A 132 1 O MET A 131 N THR A 114 SHEET 1 B 5 ASN B 68 VAL B 70 0 SHEET 2 B 5 THR B 34 SER B 38 1 N LEU B 37 O VAL B 70 SHEET 3 B 5 ASP B 6 PHE B 9 1 N ILE B 7 O THR B 34 SHEET 4 B 5 LEU B 111 THR B 114 1 O VAL B 113 N THR B 8 SHEET 5 B 5 THR B 130 PRO B 132 1 O MET B 131 N THR B 114 CRYST1 54.342 46.381 62.484 90.00 113.33 90.00 P 1 21 1 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 0.018402 0.000000 0.007937 0.00000 SCALE2 0.000000 0.021561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017429 0.00000