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- PDB-2khd: Solution NMR structure of VC_A0919 from Vibrio cholerae. Northeas... -

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Basic information

Entry
Database: PDB / ID: 2khd
TitleSolution NMR structure of VC_A0919 from Vibrio cholerae. Northeast Structural Genomics Consortium Target VcR52
ComponentsUncharacterized protein VC_A0919
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha beta / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
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 cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Wang, H. / Ciccosanti, C. / Jiang, M. / Liu, J. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. ...Ramelot, T.A. / Cort, J.R. / Wang, H. / Ciccosanti, C. / Jiang, M. / Liu, J. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of VC_A0919 from Vibrio cholerae. Northeast Structural Genomics Consortium Target VcR52.
Authors: Ramelot, T.A. / Cort, J.R. / Wang, H. / Ciccosanti, C. / Jiang, M. / Liu, J. / Rost, B. / Swapna, G.V.T. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionApr 2, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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 VC_A0919


Theoretical massNumber of molelcules
Total (without water)12,0561
Polymers12,0561
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 / 125structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein VC_A0919


Mass: 12055.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: El Tor Inaba N16961 / Serotype O1 / Gene: VC_A0919 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: Q9KL30

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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
1313D 1H-15N NOESY
1413D 1H-13C NOESY
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D C(CO)NH
11113D HBHA(CO)NH
11213D (H)CCH-TOCSY
11313D (H)CCH-COSY
11422D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 0.5 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
220 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 0.5 mM [U-5% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMES1
100 mMsodium chloride1
5 mMcalcium chloride1
10 mMDTT1
0.02 %sodium azide1
0.5 mMprotein[U-100% 13C; U-100% 15N]1
20 mMMES2
100 mMsodium chloride2
5 mMcalcium chloride2
10 mMDTT2
0.02 %sodium azide2
0.5 mMprotein[U-5% 13C; U-100% 15N]2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Bruker AvanceIIIBrukerAVANCE III8503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.3Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5(PDBStat) R. Tejero, G.T. Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NIH-Xplor-2.20 refinement with hydrogen bond PMF, radius of gyration, rama, IVM module.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 125 / Conformers submitted total number: 20

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