HEADER HYDROLASE 22-MAY-07 2Z2K TITLE CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-TRNA HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PTH; COMPND 5 EC: 3.1.1.29; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: RV1014C, PTH; 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: PRSETBMTUPTH KEYWDS PROTEIN SYNTHESIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SELVARAJ,S.ROY,N.S.SINGH,R.SANGEETHA,U.VARSHNEY,M.VIJAYAN REVDAT 5 01-NOV-23 2Z2K 1 REMARK REVDAT 4 13-JUL-11 2Z2K 1 VERSN REVDAT 3 24-FEB-09 2Z2K 1 VERSN REVDAT 2 04-SEP-07 2Z2K 1 JRNL REVDAT 1 24-JUL-07 2Z2K 0 JRNL AUTH M.SELVARAJ,S.ROY,N.S.SINGH,R.SANGEETHA,U.VARSHNEY,M.VIJAYAN JRNL TITL STRUCTURAL PLASTICITY AND ENZYME ACTION: CRYSTAL STRUCTURES JRNL TITL 2 OF MYCOBACTERIUM TUBERCULOSIS PEPTIDYL-TRNA HYDROLASE JRNL REF J.MOL.BIOL. V. 372 186 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17619020 JRNL DOI 10.1016/J.JMB.2007.06.053 REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 71239.550 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 5397 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) : 0.198 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 299 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.66 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 797 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 51 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.055 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1341 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -11.35000 REMARK 3 B22 (A**2) : 17.66000 REMARK 3 B33 (A**2) : -6.31000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.41 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.850 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) : 1.330 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.940 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 42.61 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 2Z2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000027440. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5428 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.38400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2PTH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15%(W/V) PEG 8000, 100MM HEPES, REMARK 280 5%(V/V) 2-PROPANOL, PH 7.5, MICROBATCH, TEMPERATURE 298K 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 17.92000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.29500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.53000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.29500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.92000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.53000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 181 REMARK 465 GLU A 182 REMARK 465 PRO A 183 REMARK 465 ALA A 184 REMARK 465 GLN A 185 REMARK 465 ASN A 186 REMARK 465 ARG A 187 REMARK 465 VAL A 188 REMARK 465 HIS A 189 REMARK 465 ALA A 190 REMARK 465 TRP A 191 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 ARG A 159 CG CD NE CZ NH1 NH2 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 16 -6.94 -57.36 REMARK 500 SER A 46 -16.57 -144.15 REMARK 500 SER A 84 71.13 45.55 REMARK 500 PHE A 101 120.49 -34.31 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 CL A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z2I RELATED DB: PDB REMARK 900 RELATED ID: 2Z2J RELATED DB: PDB DBREF 2Z2K A 1 191 UNP P65865 PTH_MYCTU 1 191 SEQRES 1 A 191 MET ALA GLU PRO LEU LEU VAL VAL GLY LEU GLY ASN PRO SEQRES 2 A 191 GLY ALA ASN TYR ALA ARG THR ARG HIS ASN LEU GLY PHE SEQRES 3 A 191 VAL VAL ALA ASP LEU LEU ALA ALA ARG LEU GLY ALA LYS SEQRES 4 A 191 PHE LYS ALA HIS LYS ARG SER GLY ALA GLU VAL ALA THR SEQRES 5 A 191 GLY ARG SER ALA GLY ARG SER LEU VAL LEU ALA LYS PRO SEQRES 6 A 191 ARG CYS TYR MET ASN GLU SER GLY ARG GLN ILE GLY PRO SEQRES 7 A 191 LEU ALA LYS PHE TYR SER VAL ALA PRO ALA ASN ILE ILE SEQRES 8 A 191 VAL ILE HIS ASP ASP LEU ASP LEU GLU PHE GLY ARG ILE SEQRES 9 A 191 ARG LEU LYS ILE GLY GLY GLY GLU GLY GLY HIS ASN GLY SEQRES 10 A 191 LEU ARG SER VAL VAL ALA ALA LEU GLY THR LYS ASP PHE SEQRES 11 A 191 GLN ARG VAL ARG ILE GLY ILE GLY ARG PRO PRO GLY ARG SEQRES 12 A 191 LYS ASP PRO ALA ALA PHE VAL LEU GLU ASN PHE THR PRO SEQRES 13 A 191 ALA GLU ARG ALA GLU VAL PRO THR ILE CYS GLU GLN ALA SEQRES 14 A 191 ALA ASP ALA THR GLU LEU LEU ILE GLU GLN GLY MET GLU SEQRES 15 A 191 PRO ALA GLN ASN ARG VAL HIS ALA TRP HET CL A1001 1 HETNAM CL CHLORIDE ION FORMUL 2 CL CL 1- FORMUL 3 HOH *78(H2 O) HELIX 1 1 GLY A 14 ALA A 18 5 5 HELIX 2 2 THR A 20 HIS A 22 5 3 HELIX 3 3 ASN A 23 GLY A 37 1 15 HELIX 4 4 TYR A 68 GLU A 71 5 4 HELIX 5 5 SER A 72 TYR A 83 1 12 HELIX 6 6 ALA A 86 ALA A 88 5 3 HELIX 7 7 HIS A 115 GLY A 126 1 12 HELIX 8 8 ASP A 145 VAL A 150 1 6 HELIX 9 9 THR A 155 GLY A 180 1 26 SHEET 1 A 7 LYS A 41 ALA A 42 0 SHEET 2 A 7 ALA A 48 SER A 55 -1 O VAL A 50 N LYS A 41 SHEET 3 A 7 ARG A 58 PRO A 65 -1 O LEU A 62 N ALA A 51 SHEET 4 A 7 LEU A 5 GLY A 9 1 N LEU A 5 O SER A 59 SHEET 5 A 7 ILE A 90 ASP A 96 1 O ILE A 91 N VAL A 8 SHEET 6 A 7 GLN A 131 GLY A 136 1 O ILE A 135 N HIS A 94 SHEET 7 A 7 ILE A 104 ILE A 108 -1 N LYS A 107 O ARG A 132 SITE 1 AC1 1 LYS A 44 CRYST1 35.840 57.060 72.590 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 0.027902 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013776 0.00000