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- PDB-2jrc: Solution structure of Peptidyl-tRNA Hydrolase from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2jrc
TitleSolution structure of Peptidyl-tRNA Hydrolase from Mycobacterium tuberculosis H37Rv.
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
KeywordsHYDROLASE / PTH / Solution structure / Mycobacterium tuberculosis H37Rv
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / plasma membrane / cytoplasm
Similarity search - Function
Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 2. / Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPulavarti, S.V.S.R.K. / Jain, A. / Pathak, P.P. / Arora, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Solution structure and dynamics of peptidyl-tRNA hydrolase from Mycobacterium tuberculosis H37Rv.
Authors: Pulavarti, S.V. / Jain, A. / Pathak, P.P. / Mahmood, A. / Arora, A.
History
DepositionJun 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)22,0121
Polymers22,0121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 135target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Peptidyl-tRNA hydrolase / Alternative ribosome-rescue factor B / PTH


Mass: 22012.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: pth / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: P65865, UniProt: P9WHN7*PLUS, peptidyl-tRNA hydrolase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-99% 13C; U-99% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-99% 13C; U-99% 15N] protein, 99.8% D2O99.8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMprotein[U-99% 13C; U-99% 15N]1
1 mMprotein[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CYANA / Version: 1.0.5 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2161 / NOE intraresidue total count: 1330 / NOE long range total count: 237 / NOE medium range total count: 161 / NOE sequential total count: 433 / Protein phi angle constraints total count: 148 / Protein psi angle constraints total count: 147
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 135 / Conformers submitted total number: 40

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