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- PDB-2kjq: Solution Structure Of Protein NMB1076 From Neisseria meningitidis... -

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Basic information

Entry
Database: PDB / ID: 2kjq
TitleSolution Structure Of Protein NMB1076 From Neisseria meningitidis. Northeast Structural Genomics Consortium Target MR101B.
ComponentsDnaA-related protein
KeywordsREPLICATION / solution structure / NESG / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


DNA replication origin binding / DNA replication initiation / negative regulation of DNA-templated DNA replication initiation / DNA replication / plasma membrane
Similarity search - Function
DnaA regulatory inactivator Hda / Chromosomal replication initiator protein DnaA / Bacterial dnaA protein / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DnaA-related protein
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, Y. / Maglaqui, M. / Eletsky, A. / Ciccosanti, C. / Sathyamoorthy, B. / Jiang, M. / Garcia, E. / Nair, R. / Rost, B. / Swapna, G. ...Wu, Y. / Maglaqui, M. / Eletsky, A. / Ciccosanti, C. / Sathyamoorthy, B. / Jiang, M. / Garcia, E. / Nair, R. / Rost, B. / Swapna, G. / Acton, T. / Xiao, R. / Everett, J. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure Of Protein NMB1076 From Neisseria meningitidis. Northeast Structural Genomics Consortium Target MR101B.
Authors: Wu, Y. / Maglaqui, M. / Eletsky, A. / Ciccosanti, C. / Sathyamoorthy, B. / Jiang, M. / Garcia, E. / Nair, R. / Rost, B. / Swapna, G. / Acton, T. / Xiao, R. / Everett, J. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaA-related protein


Theoretical massNumber of molelcules
Total (without water)17,0021
Polymers17,0021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaA-related protein


Mass: 17002.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: NMB1076 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9JZF5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D CCH-TOCSY
1813D 15N-13C RESOLVED SIMULTANIOUS NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-5% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein-1[U-5% 13C; U-100% 15N]1
1.0 mMprotein-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.5 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.peak picking
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
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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