HEADER HYDROLASE 23-DEC-15 2NAF TITLE SOLUTION STRUCTURE OF 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 GENE: MSMEG_5432, MSMEI_5283, PTH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PETNH6 KEYWDS PROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.YADAV,P.PATHAK,F.FATMA,A.KABRA,S.PULAVARTI,A.JAIN,A.KUMAR,V.SHUKLA, AUTHOR 2 A.ARORA REVDAT 3 15-MAY-24 2NAF 1 REMARK REVDAT 2 14-JUN-23 2NAF 1 REMARK REVDAT 1 11-JAN-17 2NAF 0 JRNL AUTH A.KABRA,F.FATMA,S.SHAHID,P.P.PATHAK,R.YADAV,S.V.PULAVARTI, JRNL AUTH 2 S.TRIPATHI,A.JAIN,A.ARORA JRNL TITL STRUCTURAL CHARACTERIZATION OF PEPTIDYL-TRNA HYDROLASE FROM JRNL TITL 2 MYCOBACTERIUM SMEGMATIS BY NMR SPECTROSCOPY. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1864 1304 2016 JRNL REFN ISSN 0006-3002 JRNL PMID 27378575 JRNL DOI 10.1016/J.BBAPAP.2016.06.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CNS REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NAF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000104622. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] PROTEIN, 20 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 0.1 % SODIUM AZIDE, 1 REMARK 210 MM AEBSF PROTEASE INHIBITOR, 1 REMARK 210 MM DTT, 95% H2O/5% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] PROTEIN, REMARK 210 20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 0.1 % SODIUM REMARK 210 AZIDE, 1 MM AEBSF PROTEASE REMARK 210 INHIBITOR, 1 MM DTT, 95% H2O/5% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 0.1 % SODIUM AZIDE, 1 MM AEBSF REMARK 210 PROTEASE INHIBITOR, 1 MM DTT, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D CBCA(CO)NH; 3D HNCACB; REMARK 210 3D H(CCO)NH; 3D C(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CARA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HD21 LEU A 55 HB VAL A 60 1.28 REMARK 500 H2 MET A 1 OE1 GLU A 3 1.58 REMARK 500 OE1 GLU A 49 HZ1 LYS A 64 1.59 REMARK 500 OD2 ASP A 95 HD1 HIS A 115 1.59 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 1 ALA A 2 22.08 -166.73 REMARK 500 1 PRO A 13 96.43 -62.96 REMARK 500 1 LYS A 44 86.31 -69.23 REMARK 500 1 LYS A 45 -62.34 -173.13 REMARK 500 1 ALA A 56 -67.60 67.02 REMARK 500 1 TYR A 68 144.30 70.27 REMARK 500 1 SER A 84 90.95 63.12 REMARK 500 1 PRO A 87 93.11 -63.18 REMARK 500 1 GLN A 89 148.99 -173.64 REMARK 500 1 LEU A 108 -72.48 -66.78 REMARK 500 1 HIS A 115 -86.44 -103.14 REMARK 500 1 ASN A 129 72.63 69.85 REMARK 500 1 PHE A 130 -82.82 -140.86 REMARK 500 1 ARG A 143 -66.96 -105.53 REMARK 500 1 ALA A 156 -71.62 -92.46 REMARK 500 1 GLN A 179 -62.46 -93.46 REMARK 500 2 THR A 20 -169.50 -111.74 REMARK 500 2 ALA A 56 10.16 58.45 REMARK 500 2 TYR A 68 126.77 75.48 REMARK 500 2 PRO A 87 83.00 -58.27 REMARK 500 2 LEU A 108 -90.62 -123.59 REMARK 500 2 LYS A 128 -161.93 -120.68 REMARK 500 2 ALA A 156 -72.41 -79.60 REMARK 500 2 GLN A 179 -77.37 -100.59 REMARK 500 3 LYS A 44 88.46 -64.11 REMARK 500 3 LYS A 45 -54.97 174.22 REMARK 500 3 ALA A 56 -51.58 70.19 REMARK 500 3 TYR A 68 163.81 69.41 REMARK 500 3 LEU A 108 -132.40 -87.37 REMARK 500 3 ASN A 129 67.71 75.35 REMARK 500 3 PHE A 130 -87.87 -142.99 REMARK 500 3 HIS A 131 104.97 -161.88 REMARK 500 3 ARG A 143 -70.07 -82.01 REMARK 500 4 PRO A 15 -71.49 -55.09 REMARK 500 4 LYS A 45 -58.54 174.34 REMARK 500 4 ALA A 56 -36.83 67.60 REMARK 500 4 TYR A 68 138.27 75.27 REMARK 500 4 PRO A 87 33.28 -75.39 REMARK 500 4 LEU A 108 -71.93 -67.30 REMARK 500 4 LYS A 128 -91.70 -99.75 REMARK 500 4 ASN A 129 7.97 55.07 REMARK 500 4 PHE A 130 -90.85 -131.31 REMARK 500 4 HIS A 131 135.38 -175.92 REMARK 500 4 ARG A 143 -70.22 -83.82 REMARK 500 4 ALA A 156 -72.95 -83.93 REMARK 500 5 LYS A 45 -48.36 170.84 REMARK 500 5 ALA A 56 -27.96 68.50 REMARK 500 5 TYR A 68 115.78 66.43 REMARK 500 5 LEU A 108 -133.06 -78.59 REMARK 500 5 GLU A 112 -61.21 78.85 REMARK 500 REMARK 500 THIS ENTRY HAS 115 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25936 RELATED DB: BMRB DBREF 2NAF A 1 191 UNP A0R3D3 PTH_MYCS2 1 191 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 SER VAL VAL LEU ALA LYS PRO SEQRES 6 A 191 ARG CYS TYR 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 ALA 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 HELIX 1 1 THR A 16 HIS A 22 5 7 HELIX 2 2 ASN A 23 GLY A 37 1 15 HELIX 3 3 TYR A 68 TYR A 83 1 16 HELIX 4 4 ASN A 116 GLY A 126 1 11 HELIX 5 5 ASP A 145 LEU A 151 1 7 HELIX 6 6 GLU A 161 GLN A 179 1 19 HELIX 7 7 LEU A 181 HIS A 189 1 9 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 THR A 58 N LEU A 55 SHEET 4 A 7 PRO A 4 GLY A 9 1 N LEU A 5 O SER A 59 SHEET 5 A 7 GLN A 89 GLU A 96 1 O VAL A 91 N LEU A 6 SHEET 6 A 7 HIS A 131 GLY A 136 1 O VAL A 133 N HIS A 94 SHEET 7 A 7 ILE A 104 LYS A 107 -1 N LYS A 107 O ARG A 132 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1