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- PDB-2ba3: NMR Structure of NikA N-terminal Fragment -

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Basic information

Entry
Database: PDB / ID: 2ba3
TitleNMR Structure of NikA N-terminal Fragment
ComponentsNikA
KeywordsDNA BINDING PROTEIN / DIMER / BACTERIAL CONJUGATION / RELAXASE / DNA BINDING / RIBBON-HELIX-HELIX
Function / homologyMet repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / : / NikA protein
Function and homology information
Biological speciesPlasmid R64 (others)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYoshida, H. / Furuya, N. / Lin, Y.J. / Guntert, P. / Komano, T. / Kainosho, M.
CitationJournal: To be Published
Title: NMR Structure of NikA N-teminal Fragment
Authors: Yoshida, H. / Furuya, N. / Lin, Y.J. / Guntert, P. / Komano, T. / Kainosho, M.
History
DepositionOct 14, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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: NikA
B: NikA


Theoretical massNumber of molelcules
Total (without water)11,4652
Polymers11,4652
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 #1closest to the average

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Components

#1: Protein NikA


Mass: 5732.487 Da / Num. of mol.: 2 / Fragment: N-TERMINAL FRAGMENT(RESIDUES 1-51)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmid R64 (others) / Gene: NIKA / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: GenBank: 4903137, UniProt: Q52335*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 2mM NIKA(1-51) U-15N, 13C; 50mM phosphate buffer NA; 50mM NaCL
Solvent system: H2O and D2O
Sample conditionsIonic strength: 50mM / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.2.1Guntert et al.structure solution
OPALp1.4Koradi, R., Billeter, M., Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 20 CYANA conformers with the lowest final target function values were subjected to restrained energy minimization in explicit solvent against the AMBER force field using the program OPALp
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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