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- PDB-2fki: NMR Structure of Protein yjbR from Escherichia coli; Northeast St... -

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Basic information

Entry
Database: PDB / ID: 2fki
TitleNMR Structure of Protein yjbR from Escherichia coli; Northeast Structural Genomics Consortium Target ER226
ComponentsProtein yjbR
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / ER226 / GFT-NMR / ALPHA-BETA / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyAspartate Aminotransferase, domain 1 - #30 / Uncharacterised protein YjbR / YjbR-like superfamily / YjbR / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / Uncharacterized protein YjbR
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics torsion angle dynamics
AuthorsSingarapu, K.K. / Liu, G. / Xiao, R. / Shetty, K.G. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2007
Title: NMR structure of protein yjbR from Escherichia coli reveals 'double-wing' DNA binding motif.
Authors: Singarapu, K.K. / Liu, G. / Xiao, R. / Bertonati, C. / Honig, B. / Montelione, G.T. / Szyperski, T.
History
DepositionJan 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 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: Protein yjbR


Theoretical massNumber of molelcules
Total (without water)14,6081
Polymers14,6081
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 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein yjbR


Mass: 14607.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yjbR / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK / References: UniProt: P0AF50

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111[4,3]D GFT, HNNCABCA
121[4,3]D GFT, CABCA(CO)NHN
131[4,3]D GFT ali-(H)CCH
141[4,3]D GFT aro-(H)CCH
151[4,3]D GFT, HABCAB(CO)NHN
161SIMULTANEOUS HETERONUCLEAR RESOLVED [1H, 1H]-NOESY

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Sample preparation

DetailsContents: U-15N, 13C; 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5, 5% D2O, 95% H2O.
Solvent system: 5% D2O, 95% H2O.
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: ambient / Temperature: 298 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 INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.5Bax, A., Delaglio, F.processing
XEASY1.3.13Wuthrich, K., et aldata analysis
DYANA1.5Guntert, P., Wuthrich, K.data analysis
CYANA2.1Guntert, P., et alrefinement
AutoStructure2.0.0Montelione, G.T., et aldata analysis
CNS1.1Brunger, A.T. et alrefinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 2100 restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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