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- PDB-2js4: Solution NMR Structure of Bordetella bronchiseptica protein BB200... -

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Basic information

Entry
Database: PDB / ID: 2js4
TitleSolution NMR Structure of Bordetella bronchiseptica protein BB2007. Northeast Structural Genomics Consortium target BoR54
ComponentsUPF0434 protein BB2007
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / Northeast Structural Genomics Consortium / beta / PSI-2 / Protein Structure Initiative
Function / homologyTrm112-like / Trm112p-like protein / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Mainly Beta / UPF0434 protein BB2007
Function and homology information
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsEletsky, A. / Sukumaran, D. / Wu, Y. / Singarapu, K. / Parish, D. / Xu, D. / Wang, D. / Nwosu, C. / Cunningham, K. / Xiao, R. ...Eletsky, A. / Sukumaran, D. / Wu, Y. / Singarapu, K. / Parish, D. / Xu, D. / Wang, D. / Nwosu, C. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR Solution Structure of Bordetella bronchiseptica protein BB2007.
Authors: Eletsky, A. / Szyperski, T.
History
DepositionJun 29, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 10, 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_software ...database_2 / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0434 protein BB2007


Theoretical massNumber of molelcules
Total (without water)7,8891
Polymers7,8891
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein UPF0434 protein BB2007


Mass: 7889.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Species: Bordetella bronchiseptica / Strain: RB50, NCTC 13252 / Gene: BB2007 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): XL10 / References: UniProt: Q7WKU6

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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 HNCO
1413D HN(CA)CB
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D (H)CCH-COSY
1913D 1H-13C,15N NOESY
11013D (H)CCH-COSY
11122D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM [U-100% 13C; U-100% 15N] protein, 0.02 % NaN3, 100 mM DTT, 5 mM CaCl2, 100 mM NaCl, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-5% 13C; U-100% 15N] protein, 0.02 % NaN3, 100 mM DTT, 5 mM CaCl2, 100 mM NaCl, 20 mM MES, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.3 mMBoR54[U-100% 13C; U-100% 15N]1
0.02 %NaN31
100 mMDTT1
5 mMCaCl21
100 mMNaCl1
20 mMMES1
0.8 mMBoR54[U-5% 13C; U-100% 15N]2
0.02 %NaN32
100 mMDTT2
5 mMCaCl22
100 mMNaCl2
20 mMMES2
Sample conditionsIonic strength: 0.115 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
PROSA6.0.2Guntertprocessing
CARA1.8.4R. Kellerdata analysis
CSI2David Wishartdata analysis
CSI22Brian Sykesdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.0.0Huang, Tejero, Powers and Montelionestructure solution
AutoAssign1.15.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: simulated annealing in explicit water bath
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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