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- PDB-2lgj: Solution structure of MsPTH -

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Basic information

Entry
Database: PDB / ID: 2lgj
TitleSolution structure of MsPTH
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / MsPTH
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 (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsYadav, R. / Pathak, P. / Pulavarti, S. / Jain, A. / Kumar, A. / Shukla, V. / Arora, A.
CitationJournal: To be Published
Title: Solution structure and backbone dynamics of Peptidyl t-RNA hydrolase from Mycobacterium smegmatis
Authors: Yadav, R. / Pathak, P. / Pulavarti, S. / Jain, A. / Kumar, A. / Shukla, V. / Arora, A.
History
DepositionJul 27, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-tRNA hydrolase / PTH / MsPTH


Mass: 20306.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: pth / Production host: Escherichia coli (E. coli) / 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 HN(CA)CB
1323D CBCA(CO)NH
1423D HNCA
1523D HNCO
1623D HN(CA)CO
1723D H(CCO)NH
1823D C(CO)NH
1923D (H)CCH-TOCSY
11013D 1H-15N NOESY
11132D 1H-13C HSQC aliphatic
11232D 1H-13C HSQC aromatic
11333D 1H-13C NOESY aliphatic
11432D 1H-13C NOESY aromatic
1152HB(CBCGCE)HE
1162HB(CBCGCD)HD

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-98% 15N] MsPTH-1, 20mM sodium phosphate-2, 50mM sodium chloride-3, 1mM DTT-4, 1mM AEBSF protease inhibitor-5, 1% sodium azide-6, 93% H2O/7% D2O93% H2O/7% D2O
21mM [U-98% 13C; U-98% 15N] MsPTH-7, 20mM sodium phosphate-8, 50mM sodium chloride-9, 1mM DTT-10, 1mM AEBSF protease inhibitor-11, 1% sodium azide-12, 93% H2O/7% D2O93% H2O/7% D2O
30.9mM [U-98% 13C; U-98% 15N] MsPTH-13, 20mM sodium phosphate-14, 50mM sodium chloride-15, 1mM DTT-16, 1mM AEBSF protease inhibitor-17, 1% sodium azide-18, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMsPTH-1[U-98% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
1 mMAEBSF protease inhibitor-51
1 %sodium azide-61
1 mMMsPTH-7[U-98% 13C; U-98% 15N]2
20 mMsodium phosphate-82
50 mMsodium chloride-92
1 mMDTT-102
1 mMAEBSF protease inhibitor-112
1 %sodium azide-122
0.9 mMMsPTH-13[U-98% 13C; U-98% 15N]3
20 mMsodium phosphate-143
50 mMsodium chloride-153
1 mMDTT-163
1 mMAEBSF protease inhibitor-173
1 %sodium azide-183
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 software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2188
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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