HEADER HYDROLASE 04-NOV-09 3KJZ TITLE CRYSTAL STRUCTURE OF NATIVE PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM TITLE 2 SMEGMATIS 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 SMEGMATIS STR. MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: ATCC 700084 / MC(2)155; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN SYNTHESIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KUMAR,N.SINGH,R.YADAV,R.PREM KUMAR,S.SHARMA,A.ARORA,T.P.SINGH REVDAT 3 01-NOV-23 3KJZ 1 REMARK REVDAT 2 05-AUG-20 3KJZ 1 JRNL REVDAT 1 18-AUG-10 3KJZ 0 JRNL AUTH A.KUMAR,N.SINGH,R.YADAV,R.P.KUMAR,S.SHARMA,A.ARORA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM JRNL TITL 2 MYCOBACTERIUM SMEGMATIS REVEALS NOVEL FEATURES RELATED TO JRNL TITL 3 ENZYME DYNAMICS. JRNL REF INT J BIOCHEM MOL BIOL V. 3 58 2012 JRNL REFN ESSN 2152-4114 JRNL PMID 22509481 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 87674.530 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 6501 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) : 0.182 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 362 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1015 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.3500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 59 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.046 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1428 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 141 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.70000 REMARK 3 B22 (A**2) : -2.07000 REMARK 3 B33 (A**2) : 0.37000 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) : 0.24 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.37 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.910 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) : 2.790 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.270 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.750 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.210 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 51.57 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3KJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 291 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR 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 : 6501 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 23.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PDB ENTRY 2Z2I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MM TRIS-HCL, 1MM EDTA, 50MM NACL, REMARK 280 10% ISOPROPANOL, 30% PEG 1500, 5MM 2-MERCAPTOETHANOL, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, 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 22.50500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.01000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.49000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.01000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.50500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.49000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 4 C - N - CD ANGL. DEV. = -14.4 DEGREES REMARK 500 PRO A 4 CA - N - CD ANGL. DEV. = -9.2 DEGREES REMARK 500 PRO A 4 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 PRO A 13 C - N - CA ANGL. DEV. = 10.4 DEGREES REMARK 500 PRO A 13 CA - N - CD ANGL. DEV. = -10.7 DEGREES REMARK 500 GLY A 14 C - N - CA ANGL. DEV. = -18.4 DEGREES REMARK 500 PRO A 140 C - N - CD ANGL. DEV. = -21.5 DEGREES REMARK 500 GLY A 142 N - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 2 -32.27 -130.64 REMARK 500 GLU A 3 78.05 34.48 REMARK 500 PRO A 4 179.38 -59.64 REMARK 500 HIS A 22 0.39 -66.16 REMARK 500 MET A 69 -66.15 -27.70 REMARK 500 PRO A 141 85.67 -54.67 REMARK 500 ARG A 143 -8.67 -150.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z2K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM MYCOBACTERIUM REMARK 900 TUBERCULOSIS REMARK 900 RELATED ID: 3KK0 RELATED DB: PDB REMARK 900 PARTIALLY FOLDED INTERMEDIATE STATE OF PEPTIDYL-TRNA HYDROLASE FROM REMARK 900 MYCOBACTERIUM SMEGMATIS REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE ARE CONFLICTS BETWEEN THE REPORTED SEQUENCE AND DATABASE REMARK 999 REFERENCE SEQUENCE. THE DEPOSITORS BUILT THESE RESIDUES ON THE REMARK 999 BASIS OF THE OBSERVED ELECTRON DENSITY. DBREF 3KJZ A 1 191 UNP A0R3D3 PTH_MYCS2 1 191 SEQADV 3KJZ THR A 59 UNP A0R3D3 SER 59 SEE REMARK 999 SEQADV 3KJZ ILE A 67 UNP A0R3D3 CYS 67 SEE REMARK 999 SEQADV 3KJZ SER A 68 UNP A0R3D3 TYR 68 SEE REMARK 999 SEQADV 3KJZ SER A 156 UNP A0R3D3 ALA 156 SEE REMARK 999 SEQRES 1 A 191 MET ALA GLU PRO LEU LEU VAL VAL GLY LEU GLY ASN PRO SEQRES 2 A 191 GLY PRO THR TYR ALA LYS THR ARG HIS ASN LEU GLY PHE SEQRES 3 A 191 MET VAL ALA ASP VAL LEU ALA GLY ARG ILE GLY SER ALA SEQRES 4 A 191 PHE LYS VAL HIS LYS LYS SER GLY ALA GLU VAL VAL THR SEQRES 5 A 191 GLY ARG LEU ALA GLY THR THR VAL VAL LEU ALA LYS PRO SEQRES 6 A 191 ARG ILE SER MET ASN GLU SER GLY ARG GLN VAL GLY PRO SEQRES 7 A 191 LEU ALA LYS PHE TYR SER VAL PRO PRO GLN GLN ILE VAL SEQRES 8 A 191 VAL ILE HIS ASP GLU LEU ASP ILE ASP PHE GLY ARG ILE SEQRES 9 A 191 ARG LEU LYS LEU GLY GLY GLY GLU GLY GLY HIS ASN GLY SEQRES 10 A 191 LEU ARG SER VAL ALA SER ALA LEU GLY THR LYS ASN PHE SEQRES 11 A 191 HIS ARG VAL ARG ILE GLY VAL GLY ARG PRO PRO GLY ARG SEQRES 12 A 191 LYS ASP PRO ALA ALA PHE VAL LEU GLU ASN PHE THR SER SEQRES 13 A 191 ALA GLU ARG ALA GLU VAL PRO THR ILE VAL GLU GLN ALA SEQRES 14 A 191 ALA ASP ALA THR GLU LEU LEU ILE ALA GLN GLY LEU GLU SEQRES 15 A 191 PRO ALA GLN ASN THR VAL HIS ALA TRP FORMUL 2 HOH *141(H2 O) HELIX 1 1 THR A 20 HIS A 22 5 3 HELIX 2 2 ASN A 23 GLY A 37 1 15 HELIX 3 3 SER A 68 GLU A 71 5 4 HELIX 4 4 SER A 72 TYR A 83 1 12 HELIX 5 5 PRO A 86 GLN A 88 5 3 HELIX 6 6 HIS A 115 GLY A 126 1 12 HELIX 7 7 ASP A 145 LEU A 151 1 7 HELIX 8 8 THR A 155 ALA A 160 1 6 HELIX 9 9 GLU A 161 GLY A 180 1 20 HELIX 10 10 GLY A 180 HIS A 189 1 10 SHEET 1 A 7 LYS A 41 VAL A 42 0 SHEET 2 A 7 GLU A 49 LEU A 55 -1 O VAL A 50 N LYS A 41 SHEET 3 A 7 THR A 58 LYS A 64 -1 O VAL A 60 N GLY A 53 SHEET 4 A 7 LEU A 5 GLY A 9 1 N VAL A 7 O ALA A 63 SHEET 5 A 7 ILE A 90 GLU A 96 1 O ILE A 93 N VAL A 8 SHEET 6 A 7 HIS A 131 GLY A 136 1 O ILE A 135 N HIS A 94 SHEET 7 A 7 ILE A 104 LEU A 108 -1 N LYS A 107 O ARG A 132 CRYST1 45.010 58.980 62.020 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 0.022217 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016955 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016124 0.00000