HEADER HYDROLASE 04-FEB-22 7WT6 TITLE CRYSTAL STRUCTURE OF FULL-LENGTH PEPTIDYL-TRNA HYDROLASE FROM TITLE 2 MYCOBACTERIUM 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: MYCOBACTERIACEAE BACTERIUM; SOURCE 3 ORGANISM_TAXID: 2448780; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: PTH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENZYME CLASSIFICATION, HYDROLASE, PEPTIDYL-TRNA EXPDTA X-RAY DIFFRACTION AUTHOR R.KULANDAISAMY,U.DAS,K.K.INAMPUDI REVDAT 2 29-NOV-23 7WT6 1 REMARK REVDAT 1 13-APR-22 7WT6 0 JRNL AUTH R.KULANDAISAMY,U.DAS,K.K.INAMPUDI JRNL TITL CRYSTAL STRUCTURE OF FULL-LENGTH PEPTIDYL-TRNA HYDROLASE JRNL TITL 2 FROM MYCOBACTERIUM TUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 13638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.340 REMARK 3 FREE R VALUE TEST SET COUNT : 729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.2000 - 3.3100 0.99 2738 152 0.1568 0.1818 REMARK 3 2 3.3100 - 2.6300 1.00 2625 154 0.1725 0.2246 REMARK 3 3 2.6300 - 2.3000 1.00 2586 131 0.1718 0.2426 REMARK 3 4 2.3000 - 2.0900 0.99 2570 156 0.1771 0.2391 REMARK 3 5 2.0900 - 1.9400 0.94 2396 136 0.1918 0.2518 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.763 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.92 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.58 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1454 REMARK 3 ANGLE : 0.793 1965 REMARK 3 CHIRALITY : 0.051 215 REMARK 3 PLANARITY : 0.006 264 REMARK 3 DIHEDRAL : 6.706 878 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7WT6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027382. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976254 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : VERTICAL CRL/ HORIZONTAL REMARK 200 ELIPTICAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13646 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.937 REMARK 200 RESOLUTION RANGE LOW (A) : 37.201 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 2Z2I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 8000, 0.1M HEPES PH 7.5 REMARK 280 5% (V/V) 2-PROPANOL, MICROBATCH, TEMPERATURE 293.15K 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 18.29050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.90900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.50150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.90900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.29050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.50150 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 -10 REMARK 465 ARG A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 418 DISTANCE = 6.86 ANGSTROMS DBREF 7WT6 A 1 191 UNP P9WHN7 PTH_MYCTU 1 191 SEQADV 7WT6 MET A -10 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 ARG A -9 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 GLY A -8 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 SER A -7 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 HIS A -6 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 HIS A -5 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 HIS A -4 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 HIS A -3 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 HIS A -2 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 HIS A -1 UNP P9WHN7 EXPRESSION TAG SEQADV 7WT6 GLY A 0 UNP P9WHN7 EXPRESSION TAG SEQRES 1 A 202 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 202 GLU PRO LEU LEU VAL VAL GLY LEU GLY ASN PRO GLY ALA SEQRES 3 A 202 ASN TYR ALA ARG THR ARG HIS ASN LEU GLY PHE VAL VAL SEQRES 4 A 202 ALA ASP LEU LEU ALA ALA ARG LEU GLY ALA LYS PHE LYS SEQRES 5 A 202 ALA HIS LYS ARG SER GLY ALA GLU VAL ALA THR GLY ARG SEQRES 6 A 202 SER ALA GLY ARG SER LEU VAL LEU ALA LYS PRO ARG CYS SEQRES 7 A 202 TYR MET ASN GLU SER GLY ARG GLN ILE GLY PRO LEU ALA SEQRES 8 A 202 LYS PHE TYR SER VAL ALA PRO ALA ASN ILE ILE VAL ILE SEQRES 9 A 202 HIS ASP ASP LEU ASP LEU GLU PHE GLY ARG ILE ARG LEU SEQRES 10 A 202 LYS ILE GLY GLY GLY GLU GLY GLY HIS ASN GLY LEU ARG SEQRES 11 A 202 SER VAL VAL ALA ALA LEU GLY THR LYS ASP PHE GLN ARG SEQRES 12 A 202 VAL ARG ILE GLY ILE GLY ARG PRO PRO GLY ARG LYS ASP SEQRES 13 A 202 PRO ALA ALA PHE VAL LEU GLU ASN PHE THR PRO ALA GLU SEQRES 14 A 202 ARG ALA GLU VAL PRO THR ILE CYS GLU GLN ALA ALA ASP SEQRES 15 A 202 ALA THR GLU LEU LEU ILE GLU GLN GLY MET GLU PRO ALA SEQRES 16 A 202 GLN ASN ARG VAL HIS ALA TRP FORMUL 2 HOH *218(H2 O) HELIX 1 AA1 GLY A 14 ALA A 18 5 5 HELIX 2 AA2 THR A 20 HIS A 22 5 3 HELIX 3 AA3 ASN A 23 LEU A 36 1 14 HELIX 4 AA4 TYR A 68 GLU A 71 5 4 HELIX 5 AA5 SER A 72 SER A 84 1 13 HELIX 6 AA6 ALA A 86 ALA A 88 5 3 HELIX 7 AA7 HIS A 115 GLY A 126 1 12 HELIX 8 AA8 ALA A 148 GLU A 152 5 5 HELIX 9 AA9 THR A 155 ALA A 160 1 6 HELIX 10 AB1 GLU A 161 GLY A 180 1 20 HELIX 11 AB2 GLY A 180 HIS A 189 1 10 SHEET 1 AA1 7 LYS A 41 ALA A 42 0 SHEET 2 AA1 7 GLU A 49 SER A 55 -1 O VAL A 50 N LYS A 41 SHEET 3 AA1 7 ARG A 58 LYS A 64 -1 O LEU A 62 N ALA A 51 SHEET 4 AA1 7 LEU A 6 GLY A 9 1 N VAL A 7 O VAL A 61 SHEET 5 AA1 7 ILE A 90 ASP A 96 1 O ILE A 91 N VAL A 8 SHEET 6 AA1 7 GLN A 131 GLY A 136 1 O VAL A 133 N VAL A 92 SHEET 7 AA1 7 ILE A 104 ILE A 108 -1 N ARG A 105 O ARG A 134 CRYST1 36.581 39.003 123.818 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 0.027337 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025639 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008076 0.00000