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- PDB-2k2e: Solution NMR structure of Bordetella pertussis protein BP2786, a ... -

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Basic information

Entry
Database: PDB / ID: 2k2e
TitleSolution NMR structure of Bordetella pertussis protein BP2786, a Mth938-like domain. Northeast Structural Genomics Consortium target BeR31
ComponentsUncharacterized protein BP2786
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MTH938-like fold / COG03737 / DUF498 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyHypothetical Protein Mth938; Chain: A, / MTH938-like / NDUFAF3/Mth938 domain-containing protein / MTH938-like superfamily / Protein of unknown function (DUF498/DUF598) / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBordetella pertussis Tohama I (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsCort, J.R. / Ho, C.K. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Cort, J.R. / Ho, C.K. / Nwosu, C. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Bordetella pertussis protein BP2786, a Mth938-like domain.
Authors: Cort, J.R. / Kennedy, M.A.
History
DepositionApr 1, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein BP2786


Theoretical massNumber of molelcules
Total (without water)16,8741
Polymers16,8741
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)20 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein BP2786


Mass: 16874.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria)
Species: Bordetella pertussis / Strain: Tohama I / NCTC 13251 / Gene: BP2786 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7VV99

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1213D 1H-15N NOESY
1324D 1H-13C-13C-1H HMQC-NOESY
1413D (H)CCH-TOCSY
1513D (H)CCH-COSY
1613D HN(CA)CB
1713D CBCA(CO)NH
1813D HNCO
1912D 1H-15N HSQC
11012D 1H-13C HSQC
11123D 1H-13C NOESY
11222D 1H-13C HSQC
11322D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
1100 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 95% H2O/5% D2O95% H2O/5% D2O
2100 mM sodium chloride, 20 mM MES, 10 mM DTT, 0.02 % sodium azide, 5 mM calcium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
100 mMsodium chloride1
20 mMMES1
10 mMDTT1
0.02 %sodium azide1
5 mMcalcium chloride1
100 mMsodium chloride2
20 mMMES2
10 mMDTT2
0.02 %sodium azide2
5 mMcalcium chloride2
Sample conditionsIonic strength: 135 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Accelrys Software Inc.chemical shift assignment
Felix97Accelrys Software Inc.data analysis
Felix97Accelrys Software Inc.processing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
AutoStructureHuang, Tejero, Powers and Montelionerefinement
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
PSVSBhattacharya and Montelionerefinement
PSVSBhattacharya and Montelionestructure analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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