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- PDB-2naf: Solution structure of peptidyl-tRNA hydrolase from Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2naf
TitleSolution structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / Protein
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / 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
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsYadav, R. / Pathak, P. / Fatma, F. / Kabra, A. / Pulavarti, S. / Jain, A. / Kumar, A. / Shukla, V. / Arora, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Structural characterization of peptidyl-tRNA hydrolase from Mycobacterium smegmatis by NMR spectroscopy.
Authors: Kabra, A. / Fatma, F. / Shahid, S. / Pathak, P.P. / Yadav, R. / Pulavarti, S.V. / Tripathi, S. / Jain, A. / Arora, A.
History
DepositionDec 23, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)20,3061
Polymers20,3061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 20306.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_5432, MSMEI_5283, pth / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R3D3, peptidyl-tRNA hydrolase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HNCA
1423D CBCA(CO)NH
1523D HN(CA)CB
1623D H(CCO)NH
1723D C(CO)NH
1833D (H)CCH-TOCSY
1913D 1H-15N NOESY
11033D 1H-13C NOESY aliphatic
11133D 1H-13C NOESY aromatic
11232D 1H-13C HSQC aliphatic
11332D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] Protein, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 1 mM AEBSF protease inhibitor, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 13C; U-100% 15N] Protein, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 1 mM AEBSF protease inhibitor, 1 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-100% 13C; U-100% 15N] Protein, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % sodium azide, 1 mM AEBSF protease inhibitor, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMProtein-1[U-100% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
0.1 %sodium azide-41
1 mMAEBSF protease inhibitor-51
1 mMDTT-61
1 mMProtein-7[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-82
50 mMsodium chloride-92
0.1 %sodium azide-102
1 mMAEBSF protease inhibitor-112
1 mMDTT-122
1 mMProtein-13[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate-143
50 mMsodium chloride-153
0.1 %sodium azide-163
1 mMAEBSF protease inhibitor-173
1 mMDTT-183
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CARAKeller and Wuthrichchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2352 / Hydrogen bond constraints total count: 73 / Protein chi angle constraints total count: 17 / Protein phi angle constraints total count: 137 / Protein psi angle constraints total count: 135
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 10

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