HEADER HYDROLASE 18-JUN-05 2CWC TITLE CRYSTAL STRUCTURE OF ADP-RIBOSYLGLYCOHYDROLASE-RELATED PROTEIN FROM TITLE 2 THERMUS THERMOPHILUS HB8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLGLYCOHYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADP-RIBOSYLGLYCOHYDROLASE-RELATED PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS ALL ALPHA PROTEIN, STRUCTURAL GENOMICS, RIKEN STRUCTURAL KEYWDS 2 GENOMICS/PROTEOMICS INITIATIVE, RSGI, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.EBIHARA,S.YOKOYAMA,S.KURAMITSU,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 4 13-MAR-24 2CWC 1 REMARK REVDAT 3 13-JUL-11 2CWC 1 VERSN REVDAT 2 24-FEB-09 2CWC 1 VERSN REVDAT 1 18-DEC-05 2CWC 0 JRNL AUTH A.EBIHARA,S.YOKOYAMA,S.KURAMITSU JRNL TITL CRYSTAL STRUCTURE OF ADP-RIBOSYLGLYCOHYDROLASE-RELATED JRNL TITL 2 PROTEIN FROM THERMUS THERMOPHILUS HB8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 885234.940 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 31169 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) : 0.193 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3119 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4399 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 495 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2181 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.14000 REMARK 3 B22 (A**2) : -0.36000 REMARK 3 B33 (A**2) : 1.50000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.06 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.10 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 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) : 1.200 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.860 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.020 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.050 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 43.34 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000024698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.00000 REMARK 200 MONOCHROMATOR : SI DOUBLE-CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31755 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 43.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.22900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.990 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG6000, 0.1M TRIS, 0.1M REMARK 280 DIAMMONIUM HYDROGEN PHOSPHATE, PH 8.0, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K 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 22.10600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.46250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.97150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.46250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.10600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.97150 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 GLY A 3 REMARK 465 LEU A 4 REMARK 465 ARG A 92 REMARK 465 SER A 93 REMARK 465 ALA A 94 REMARK 465 THR A 95 REMARK 465 GLY A 96 REMARK 465 VAL A 97 REMARK 465 CYS A 98 REMARK 465 PHE A 99 REMARK 465 GLY A 100 REMARK 465 LEU A 101 REMARK 465 GLY A 102 REMARK 465 HIS A 103 REMARK 465 PRO A 301 REMARK 465 ARG A 302 REMARK 465 GLU A 303 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 ARG A 72 33.87 -141.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TTK003001307 RELATED DB: TARGETDB DBREF 2CWC A 1 303 UNP Q5SMG9 Q5SMG9_THET8 1 303 SEQRES 1 A 303 MET LYS GLY LEU LYS GLU ARG GLN ASP ARG ARG LEU GLY SEQRES 2 A 303 ALA PHE LEU GLY LEU ALA VAL GLY ASP ALA LEU GLY ALA SEQRES 3 A 303 GLN VAL GLU GLY LEU PRO LYS GLY THR PHE PRO GLU VAL SEQRES 4 A 303 ARG GLU MET LYS GLY GLY GLY PRO HIS ARG LEU PRO PRO SEQRES 5 A 303 GLY PHE TRP THR ASP ASP THR SER GLN ALA LEU CYS LEU SEQRES 6 A 303 ALA GLU SER LEU LEU GLN ARG GLY PHE ASP PRO LYS ASP SEQRES 7 A 303 GLN MET ASP ARG TYR LEU ARG TRP TYR ARG GLU GLY TYR SEQRES 8 A 303 ARG SER ALA THR GLY VAL CYS PHE GLY LEU GLY HIS ALA SEQRES 9 A 303 THR ARG ARG ALA LEU GLU ARG TYR ALA ALA THR GLY ASP SEQRES 10 A 303 PRO TYR ALA GLY ASP GLU ALA GLY ALA GLY ASN GLY PRO SEQRES 11 A 303 LEU MET ARG LEU ALA PRO LEU VAL LEU ALA TYR GLU ASN SEQRES 12 A 303 HIS PRO ASP LEU LEU SER LEU ALA ARG ARG ALA ALA ARG SEQRES 13 A 303 THR THR HIS GLY ALA ARG GLU ALA LEU GLU ALA THR GLU SEQRES 14 A 303 VAL LEU ALA TRP LEU LEU ARG GLU ALA LEU ARG GLY ALA SEQRES 15 A 303 PRO LYS GLU ALA LEU LEU ALA LEU GLU PRO PHE ARG GLY SEQRES 16 A 303 ALA ASP LEU HIS PRO ALA LEU ARG ARG VAL VAL GLU GLY SEQRES 17 A 303 GLY PHE TRP GLU ALA PRO GLU GLU GLY PRO GLY TYR ALA SEQRES 18 A 303 PRO GLY THR LEU ALA ALA ALA LEU TRP ALA PHE ALA ARG SEQRES 19 A 303 GLY ARG ASP PHE GLU GLU GLY MET ARG LEU ALA VAL ASN SEQRES 20 A 303 LEU GLY GLY ASP ALA ASP THR VAL GLY ALA VAL TYR GLY SEQRES 21 A 303 GLN LEU ALA GLY ALA TYR TYR GLY LEU GLY ALA ILE PRO SEQRES 22 A 303 GLY ARG TRP LEU ARG ALA LEU HIS LEU ARG GLU GLU MET SEQRES 23 A 303 GLU ALA LEU ALA LEU ALA LEU TYR ARG MET SER MET ALA SEQRES 24 A 303 SER PRO ARG GLU FORMUL 2 HOH *220(H2 O) HELIX 1 1 LYS A 5 GLN A 27 1 23 HELIX 2 2 THR A 56 GLY A 73 1 18 HELIX 3 3 ASP A 75 GLU A 89 1 15 HELIX 4 4 ALA A 104 GLY A 116 1 13 HELIX 5 5 ASN A 128 MET A 132 5 5 HELIX 6 6 ARG A 133 GLU A 142 1 10 HELIX 7 7 ASP A 146 THR A 157 1 12 HELIX 8 8 ALA A 161 ARG A 180 1 20 HELIX 9 9 PRO A 183 LEU A 190 1 8 HELIX 10 10 GLU A 191 ARG A 194 5 4 HELIX 11 11 HIS A 199 GLU A 207 1 9 HELIX 12 12 GLY A 208 GLU A 212 5 5 HELIX 13 13 TYR A 220 GLY A 235 1 16 HELIX 14 14 ASP A 237 ASN A 247 1 11 HELIX 15 15 ASP A 251 GLY A 268 1 18 HELIX 16 16 LEU A 269 ILE A 272 5 4 HELIX 17 17 PRO A 273 LEU A 280 1 8 HELIX 18 18 LEU A 282 MET A 298 1 17 CRYST1 44.212 73.943 78.925 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 0.022618 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012670 0.00000