HEADER HYDROLASE 11-JAN-14 2MJL TITLE SOLUTION STRUCTURE OF PEPTIDYL-TRNA HYROLASE FROM VIBRIO CHOLERAE 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: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 579112; SOURCE 4 STRAIN: M66-2; SOURCE 5 GENE: PTH, VCM66_2107; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-NH6 KEYWDS HYDROLASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.KABRA,S.SHAHID,R.YADAV,S.PULAVARTI,V.K.SHUKLA,A.ARORA REVDAT 2 14-JUN-23 2MJL 1 REMARK SEQADV REVDAT 1 21-JAN-15 2MJL 0 JRNL AUTH A.KABRA,S.SHAHID,R.YADAV,S.PULAVARTI,V.K.SHUKLA,A.ARORA JRNL TITL SOLUTION STRUCTURE OF PEPTIDYL-TRNA HYDROLASE FROM VIBRIO JRNL TITL 2 CHOLERAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CNS REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MJL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000103691. 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 : 0.9 MM [U-100% 13C; U-100% 15N] REMARK 210 VCPTH, 20 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 0.1 % REMARK 210 SODIUM AZIDE, 1 MM DTT, 93% H2O/ REMARK 210 7% D2O; 0.9 MM [U-100% 15N] REMARK 210 VCPTH, 20 MM SODIUM PHOSPHATE, REMARK 210 50 MM SODIUM CHLORIDE, 0.1 % REMARK 210 SODIUM AZIDE, 1 MM DTT, 93% H2O/ REMARK 210 7% D2O; 0.9 MM [U-100% 13C; U- REMARK 210 100% 15N] VCPTH, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 0.1 % SODIUM AZIDE, 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; 2D 1H-13C HSQC; 2D 1H-13C REMARK 210 HSQC AROMATIC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D-HN(CA)CO; REMARK 210 2D-CBHE; 2D-CBHD REMARK 210 SPECTROMETER FIELD STRENGTH : 600 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 : PSVS, NMRPIPE REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 HD2 HIS A 38 HB VAL A 40 1.31 REMARK 500 HZ2 LYS A 121 OD2 ASP A 122 1.59 REMARK 500 O ASN A 189 HG1 THR A 193 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 PRO A 5 -174.68 -68.66 REMARK 500 1 ALA A 13 -168.36 -164.28 REMARK 500 1 HIS A 24 37.48 -77.58 REMARK 500 1 PHE A 49 61.13 65.37 REMARK 500 1 ASN A 58 -66.93 66.66 REMARK 500 1 SER A 59 -26.41 -157.07 REMARK 500 1 MET A 71 -73.65 -95.75 REMARK 500 2 HIS A 24 34.95 -76.27 REMARK 500 2 ASN A 58 -64.43 70.64 REMARK 500 2 SER A 59 0.71 -163.79 REMARK 500 2 MET A 71 -70.28 -91.61 REMARK 500 2 GLU A 132 39.40 -79.19 REMARK 500 3 PRO A 15 37.69 -82.09 REMARK 500 3 HIS A 24 36.45 -74.81 REMARK 500 3 ASN A 58 -82.53 62.71 REMARK 500 3 SER A 59 9.97 -157.88 REMARK 500 3 GLU A 132 48.94 -71.32 REMARK 500 4 VAL A 2 -88.79 76.14 REMARK 500 4 SER A 3 -63.16 171.91 REMARK 500 4 LYS A 7 -75.45 -82.02 REMARK 500 4 ALA A 13 -166.53 -168.14 REMARK 500 4 LYS A 21 47.60 -80.08 REMARK 500 4 HIS A 24 35.74 -79.35 REMARK 500 4 ASN A 58 -73.29 66.35 REMARK 500 4 GLN A 86 28.59 48.87 REMARK 500 4 LYS A 131 36.04 -80.15 REMARK 500 4 PRO A 143 98.51 -55.46 REMARK 500 4 ALA A 196 84.81 -66.55 REMARK 500 5 LYS A 7 -71.09 -90.03 REMARK 500 5 ALA A 13 -144.08 -136.78 REMARK 500 5 PRO A 15 29.30 -77.94 REMARK 500 5 LYS A 47 -46.24 72.77 REMARK 500 5 ASN A 58 -83.63 63.08 REMARK 500 5 THR A 68 -72.68 -70.31 REMARK 500 5 GLN A 86 19.91 58.71 REMARK 500 6 PHE A 49 77.53 80.09 REMARK 500 6 ASN A 58 -85.63 60.25 REMARK 500 6 MET A 71 -71.45 -97.84 REMARK 500 6 GLN A 86 -15.74 72.04 REMARK 500 6 PRO A 103 32.43 -70.91 REMARK 500 7 HIS A 24 34.18 -85.71 REMARK 500 7 ASN A 58 -77.51 61.71 REMARK 500 7 SER A 59 12.26 -155.05 REMARK 500 7 MET A 71 -71.08 -97.17 REMARK 500 7 GLN A 86 69.39 38.15 REMARK 500 7 ASN A 130 -107.68 67.30 REMARK 500 8 HIS A 24 38.11 -88.06 REMARK 500 8 PHE A 49 61.82 71.60 REMARK 500 8 ASN A 58 -66.30 65.91 REMARK 500 8 SER A 59 -28.52 -162.80 REMARK 500 REMARK 500 THIS ENTRY HAS 65 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19731 RELATED DB: BMRB DBREF 2MJL A 3 197 UNP C3LPI9 PTH_VIBCM 2 196 SEQADV 2MJL MET A 1 UNP C3LPI9 EXPRESSION TAG SEQADV 2MJL VAL A 2 UNP C3LPI9 EXPRESSION TAG SEQRES 1 A 197 MET VAL SER GLN PRO ILE LYS LEU LEU VAL GLY LEU ALA SEQRES 2 A 197 ASN PRO GLY PRO GLU TYR ALA LYS THR ARG HIS ASN ALA SEQRES 3 A 197 GLY ALA TRP VAL VAL GLU GLU LEU ALA ARG ILE HIS ASN SEQRES 4 A 197 VAL THR LEU LYS ASN GLU PRO LYS PHE PHE GLY LEU THR SEQRES 5 A 197 GLY ARG LEU LEU ILE ASN SER GLN GLU LEU ARG VAL LEU SEQRES 6 A 197 ILE PRO THR THR PHE MET ASN LEU SER GLY LYS ALA ILE SEQRES 7 A 197 ALA ALA LEU ALA ASN PHE TYR GLN ILE LYS PRO GLU GLU SEQRES 8 A 197 ILE MET VAL ALA HIS ASP GLU LEU ASP LEU PRO PRO GLY SEQRES 9 A 197 VAL ALA LYS PHE LYS GLN GLY GLY GLY HIS GLY GLY HIS SEQRES 10 A 197 ASN GLY LEU LYS ASP THR ILE SER LYS LEU GLY ASN ASN SEQRES 11 A 197 LYS GLU PHE TYR ARG LEU ARG LEU GLY ILE GLY HIS PRO SEQRES 12 A 197 GLY HIS LYS ASP LYS VAL ALA GLY TYR VAL LEU GLY LYS SEQRES 13 A 197 ALA PRO ALA LYS GLU GLN GLU CYS LEU ASP ALA ALA VAL SEQRES 14 A 197 ASP GLU SER VAL ARG CYS LEU GLU ILE LEU MET LYS ASP SEQRES 15 A 197 GLY LEU THR LYS ALA GLN ASN ARG LEU HIS THR PHE LYS SEQRES 16 A 197 ALA GLU HELIX 1 1 GLY A 16 LYS A 21 1 6 HELIX 2 2 ASN A 25 ASN A 39 1 15 HELIX 3 3 ASN A 72 GLN A 86 1 15 HELIX 4 4 LYS A 88 GLU A 90 5 3 HELIX 5 5 HIS A 117 LYS A 126 1 10 HELIX 6 6 VAL A 149 LEU A 154 1 6 HELIX 7 7 PRO A 158 ASP A 182 1 25 HELIX 8 8 GLY A 183 HIS A 192 1 10 SHEET 1 A 7 LYS A 43 ASN A 44 0 SHEET 2 A 7 GLY A 50 ILE A 57 -1 O THR A 52 N LYS A 43 SHEET 3 A 7 GLN A 60 PRO A 67 -1 O LEU A 62 N LEU A 55 SHEET 4 A 7 LEU A 8 LEU A 12 1 N LEU A 9 O ARG A 63 SHEET 5 A 7 ILE A 92 GLU A 98 1 O ALA A 95 N VAL A 10 SHEET 6 A 7 TYR A 134 GLY A 139 1 O LEU A 136 N VAL A 94 SHEET 7 A 7 ALA A 106 GLN A 110 -1 N LYS A 107 O ARG A 137 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