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- PDB-2jz5: NMR solution structure of protein VPA0419 from Vibrio parahaemoly... -

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Basic information

Entry
Database: PDB / ID: 2jz5
TitleNMR solution structure of protein VPA0419 from Vibrio parahaemolyticus. Northeast Structural Genomics target VpR68
ComponentsUncharacterized protein VPA0419
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / GFT NMR / PROTEIN STRUCTURE / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyConserved hypothetical protein CHP00743 / Protein of unknown function (DUF406) / Alpha-Beta Plaits - #860 / UPF0234-like, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / cytosol / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsSingarapu, K.K. / Sukumaran, D.K. / Eletski, A. / Parish, D. / Zhao, L. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. ...Singarapu, K.K. / Sukumaran, D.K. / Eletski, A. / Parish, D. / Zhao, L. / Jiang, M. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2010
Title: Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.
Authors: Singarapu, K.K. / Mills, J.L. / Xiao, R. / Acton, T. / Punta, M. / Fischer, M. / Honig, B. / Rost, B. / Montelione, G.T. / Szyperski, T.
History
DepositionDec 28, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 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: Uncharacterized protein VPA0419


Theoretical massNumber of molelcules
Total (without water)10,3021
Polymers10,3021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein VPA0419


Mass: 10301.583 Da / Num. of mol.: 1 / Fragment: Residues 17-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VPA0419 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87J34

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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
1314,3 D GFT HNNACBCA
1414,3 D GFT CABCACONHN
1514,3D HABCAB(CO)NHN
1614,3D GFT (H)CCH COSY
1713D (H)CCH-COSY
1813D simNOESY

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Sample preparation

DetailsContents: 1.07 mM [U-100% 13C; U-100% 15N] protein VPA0419, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.07 mM / Component: Protein VPA0419 / 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionechemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata processing
PSVSBhattacharya and Montelionevalidation
TALOSCornilescu, Delaglio and Baxdata analysis
VnmrJVariandata collection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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