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- PDB-2exn: Solution structure for the protein coded by gene locus BB0938 of ... -

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Basic information

Entry
Database: PDB / ID: 2exn
TitleSolution structure for the protein coded by gene locus BB0938 of Bordetella bronchiseptica. Northeast Structural Genomics target BoR11.
ComponentsHypothetical protein BoR11
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Beta barrel containing fold / AutoStructure / AutoAssign / NMR structure / BoR11 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyMOSC, N-terminal beta barrel / MOSC N-terminal beta barrel domain / MOSC_N domain-containing protein / MOSC_N domain-containing protein
Function and homology information
Biological speciesBordetella bronchiseptica (bacteria)
MethodSOLUTION NMR / CS assignment: Backbone AutoAssign, manual sidechain HcCH-COSY, TOCSYs. AutoStructure for noesy assign. Hyper Dihedral, Dyana, Xplor(nih), and CNS force-field for simulated annealing (Dyana,xplor run within AutoStructure GUI)
AuthorsRossi, P. / Ramelot, T. / Xiao, R. / Ho, C.K. / Ma, L.-C. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biomol.NMR / Year: 2005
Title: (1)H, (13)C, and (15)N Resonance Assignments for the Protein Coded by Gene Locus BB0938 of Bordetella bronchiseptica
Authors: Rossi, P. / Ramelot, T. / Xiao, R. / Ho, C.K. / Ma, L.-C. / Acton, T.B. / Kennedy, M.A. / Montelione, G.T.
History
DepositionNov 8, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionNov 15, 2005ID: 2B2M
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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: Hypothetical protein BoR11


Theoretical massNumber of molelcules
Total (without water)15,2961
Polymers15,2961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 56target function
RepresentativeModel #1lowest target function

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Components

#1: Protein Hypothetical protein BoR11


Mass: 15296.335 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB0938 / Plasmid: pBoR11-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: Q7WNU7, UniProt: A0A0H3LRM9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1324D 13C-separated NOESY
143HNCA-J
153Hi-Res 13C-HSQC for VL stereospecific
163het-NOE
NMR detailsText: AutoQF scores after CNS with explicit H2O refinement: final M-score: 0.188 final dp-score: 0.73 (recall=0.986, precision=0.857, F-measure=0.917)

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM BoR11 (U-13C,15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.55% D2O, 95% H2O
20.5mM BoR11 (U-13C,15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.599.9% D2O
30.8mM BoR11 (5% 13C,U-15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.55% D2O, 95% H2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 6.5 / Pressure: atmospheric atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003
Bruker AVANCEBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVarian Inc.collection
XwinNMR3.5Bruker Biospin AGcollection
NMRPipe2.1Delagliodata analysis
AutoStructure2.1.1Huang, Montelionestructure solution
AutoAssign1.15Zimmerman, Moseley, Montelionedata analysis
Sparky3.91Goddarddata analysis
CNS1.1Brungerrefinement
xplor(nih)2.0.6Schwieters, Clorestructure solution
DYANA1.5Guntertstructure solution
RefinementMethod: CS assignment: Backbone AutoAssign, manual sidechain HcCH-COSY, TOCSYs. AutoStructure for noesy assign. Hyper Dihedral, Dyana, Xplor(nih), and CNS force-field for simulated annealing ...Method: CS assignment: Backbone AutoAssign, manual sidechain HcCH-COSY, TOCSYs. AutoStructure for noesy assign. Hyper Dihedral, Dyana, Xplor(nih), and CNS force-field for simulated annealing (Dyana,xplor run within AutoStructure GUI)
Software ordinal: 1
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 56 / Conformers submitted total number: 10

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