HEADER HYDROLASE 16-MAY-01 1J7G TITLE STRUCTURE OF YIHZ FROM HAEMOPHILUS INFLUENZAE (HI0670), A D-TYR- TITLE 2 TRNA(TYR) DEACYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-TYROSYL-TRNA(TYR) DEACYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE RD KW20; SOURCE 3 ORGANISM_TAXID: 71421; SOURCE 4 STRAIN: KW20; SOURCE 5 GENE: HI0670; 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: PET15B; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B-HI0670 KEYWDS D-TYR-TRNA(TYR) DEACYLASE, STRUCTURAL GENOMICS, HYPOTHETICAL PROTEIN, KEYWDS 2 STRUCTURE 2 FUNCTION PROJECT, S2F, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LIM,O.HERZBERG,STRUCTURE 2 FUNCTION PROJECT (S2F) REVDAT 4 07-FEB-24 1J7G 1 REMARK REVDAT 3 13-JUL-11 1J7G 1 VERSN REVDAT 2 24-FEB-09 1J7G 1 VERSN REVDAT 1 22-APR-03 1J7G 0 JRNL AUTH K.LIM,A.TEMPCZYK,N.BONANDER,J.TOEDT,A.HOWARD,E.EINSENSTEIN, JRNL AUTH 2 O.HERZBERG JRNL TITL A CATALYTIC MECHANISM FOR D-TYR-TRNATYR DEACYLASE BASED ON JRNL TITL 2 THE CRYSTAL STRUCTURE OF HEMOPHILUS INFLUENZAE HI0670 JRNL REF J.BIOL.CHEM. V. 278 13496 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12571243 JRNL DOI 10.1074/JBC.M213150200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.SOUTOURINA,P.PLATEAU,F.DELORT,A.PEIROTES,S.BLANQUET REMARK 1 TITL FUNCTIONAL CHARACTERIZATION OF THE D-TYR-TRNA(TYR) DEACYLASE REMARK 1 TITL 2 FROM ESCHERICHIA COLI REMARK 1 REF J.BIOL.CHEM. V. 274 19109 1999 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.274.27.19109 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 23308 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1352 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL 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 : 1115 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 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 1J7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-01. REMARK 100 THE DEPOSITION ID IS D_1000013454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25510 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.00 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 0.13500 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: SAS REMARK 200 SOFTWARE USED: SOLVE, MLPHARE, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS, 0.1 MM DTT, 0.1 MM EDTA, REMARK 280 PH 7.5, CRYSTAL FORMED DURING DIALYSIS OF PROTEIN (2.8MG/ML), REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 64.37500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.73500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.18750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.73500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.73500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 96.56250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.73500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.73500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.18750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.73500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.73500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 96.56250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.37500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 36 -4.57 83.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HI0670 RELATED DB: TARGETDB DBREF 1J7G A 1 144 UNP P44814 DTD_HAEIN 1 144 SEQRES 1 A 144 MET ILE ALA LEU ILE GLN ARG VAL SER GLN ALA LYS VAL SEQRES 2 A 144 ASP VAL LYS GLY GLU THR ILE GLY LYS ILE GLY LYS GLY SEQRES 3 A 144 LEU LEU VAL LEU LEU GLY VAL GLU LYS GLU ASP ASN ARG SEQRES 4 A 144 GLU LYS ALA ASP LYS LEU ALA GLU LYS VAL LEU ASN TYR SEQRES 5 A 144 ARG ILE PHE SER ASP GLU ASN ASP LYS MET ASN LEU ASN SEQRES 6 A 144 VAL GLN GLN ALA GLN GLY GLU LEU LEU ILE VAL SER GLN SEQRES 7 A 144 PHE THR LEU ALA ALA ASP THR GLN LYS GLY LEU ARG PRO SEQRES 8 A 144 SER PHE SER LYS GLY ALA SER PRO ALA LEU ALA ASN GLU SEQRES 9 A 144 LEU TYR GLU TYR PHE ILE GLN LYS CYS ALA GLU LYS LEU SEQRES 10 A 144 PRO VAL SER THR GLY GLN PHE ALA ALA ASP MET GLN VAL SEQRES 11 A 144 SER LEU THR ASN ASP GLY PRO VAL THR PHE TRP LEU ASN SEQRES 12 A 144 VAL FORMUL 2 HOH *207(H2 O) HELIX 1 1 ASN A 38 TYR A 52 1 15 HELIX 2 2 PHE A 79 ALA A 83 5 5 HELIX 3 3 SER A 98 GLU A 115 1 18 SHEET 1 A 3 GLN A 129 ASN A 143 0 SHEET 2 A 3 ILE A 2 VAL A 15 -1 N ALA A 3 O LEU A 142 SHEET 3 A 3 GLU A 18 ILE A 23 -1 O GLU A 18 N VAL A 15 SHEET 1 B 5 GLN A 129 ASN A 143 0 SHEET 2 B 5 ILE A 2 VAL A 15 -1 N ALA A 3 O LEU A 142 SHEET 3 B 5 GLY A 26 GLY A 32 -1 O GLY A 26 N VAL A 8 SHEET 4 B 5 GLU A 72 SER A 77 1 O GLU A 72 N LEU A 27 SHEET 5 B 5 VAL A 119 THR A 121 1 N SER A 120 O LEU A 73 SHEET 1 C 2 PHE A 55 SER A 56 0 SHEET 2 C 2 MET A 62 LEU A 64 -1 N ASN A 63 O PHE A 55 CISPEP 1 GLY A 136 PRO A 137 0 -0.82 CRYST1 55.470 55.470 128.750 90.00 90.00 90.00 P 41 21 2 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 0.018028 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007767 0.00000