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- PDB-2jn9: NMR solution structure of YkvR protein from Bacillus subtilis: NE... -

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Basic information

Entry
Database: PDB / ID: 2jn9
TitleNMR solution structure of YkvR protein from Bacillus subtilis: NESG target SR358
ComponentsYkvR protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YkvR / SR358 / Bacillus subtilis / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyYkvR-like / Protein of unknown function DUF3219 / YkvR-like superfamily / Protein of unknown function (DUF3219) / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta / Uncharacterized protein YkvR
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / distance geometry
Model type detailsminimized average
AuthorsGurla, S.V.T. / Aramini, J.M. / Chi Ho, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. / Liu, J. / Rost, B. ...Gurla, S.V.T. / Aramini, J.M. / Chi Ho, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. / Liu, J. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of YkvR protein from Bacillus subtilis: NESG target SR358
Authors: Gurla, S.V.T. / Aramini, J.M. / Chi Ho, K. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Baran, M.C. / Acton, T.B. / Liu, J. / Rost, B. / Montelione, G.T.
History
DepositionDec 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YkvR protein


Theoretical massNumber of molelcules
Total (without water)12,2441
Polymers12,2441
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 / 56structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein YkvR protein


Mass: 12243.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ykvR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic / References: UniProt: O31683

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1312D 1H-15N HSQC
1412D 1H-13C HSQC
1513D HNCO
1613D HBHA(CO)NH
1723D HNHA
1833D (H)CCH-TOCSY
1913D 1H-15N NOESY
11033D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.17 mM protein, 1.0 mM sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
21.17 mM protein, 1.0 mM sodium azide, 95% H2O, 5% D2O95% H2O/5% D2O
31.17 mM protein, 1.0 mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.0 mMsodium azide1
1.0 mMsodium azide2
1.0 mMsodium azide3
Sample conditionsIonic strength: 5.11 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.1Zimmerman, Moseley, Kulikowski, Montelionedata analysis
AVSMoseley and Montelionedata analysis
AVSMoseley and Montelioneprocessing
AutoStructureHuang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionerefinement
AutoStructureHuang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionestructure solution
DYANAGuntert, Braun and Wuthrichstructure solution
DYANAGuntert, Braun and Wuthrichrefinement
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR2.0.6Brungerrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 56 / Conformers submitted total number: 10

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