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- PDB-2jva: NMR solution structure of peptidyl-tRNA hydrolase domain protein ... -

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Basic information

Entry
Database: PDB / ID: 2jva
TitleNMR solution structure of peptidyl-tRNA hydrolase domain protein from Pseudomonas syringae pv. tomato. Northeast Structural Genomics Consortium target PsR211
ComponentsPeptidyl-tRNA hydrolase domain protein
KeywordsHYDROLASE / GFT NMR / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


translation release factor activity / hydrolase activity
Similarity search - Function
Peptide chain release factor class I superfamily / Double Stranded RNA Binding Domain - #20 / Peptide chain release factor class I / RF-1 domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase domain protein
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSingarapu, K.K. / Sukumaran, D. / Parish, D. / Eletsky, A. / Zhang, Q. / Zhao, L. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. ...Singarapu, K.K. / Sukumaran, D. / Parish, D. / Eletsky, A. / Zhang, Q. / Zhao, L. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Huang, Y.J. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2008
Title: NMR structure of the peptidyl-tRNA hydrolase domain from Pseudomonas syringae expands the structural coverage of the hydrolysis domains of class 1 peptide chain release factors.
Authors: Singarapu, K.K. / Xiao, R. / Acton, T. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionSep 14, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 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 domain protein


Theoretical massNumber of molelcules
Total (without water)12,0981
Polymers12,0981
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Peptidyl-tRNA hydrolase domain protein


Mass: 12097.713 Da / Num. of mol.: 1 / Fragment: Residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO_1818 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q885L4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1314,3D GFT CABCACONHN
1414,3D GFT HNNCABCA
1514,3D GFT (H)CCH COSY
1613D (H)CCH-COSY
1714,3D GFT HABCAB(CO)NHN
1813D sim NOESY

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Sample preparation

DetailsContents: 1.28 mM [U-100% 13C; U-100% 15N] Peptidyl-tRNA hydrolase domain protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.28 mM / Component: Peptidyl-tRNA hydrolase domain protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
TALOSCornilescu, Delaglio and Baxdata analysis
DYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionechemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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