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- PDB-2k9i: NMR structure of plasmid copy control protein ORF56 from sulfolob... -

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Basic information

Entry
Database: PDB / ID: 2k9i
TitleNMR structure of plasmid copy control protein ORF56 from sulfolobus islandicus
ComponentsUncharacterized protein ORF56
KeywordsDNA BINDING PROTEIN / plasmid copy control protein / ribbon helix helix protein
Function / homologyMet repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / regulation of DNA-templated transcription / Orthogonal Bundle / Mainly Alpha / CopG domain protein DNA-binding domain protein
Function and homology information
Biological speciesSulfolobus islandicus (archaea)
MethodSOLUTION NMR / molecular dynamics
AuthorsWeininger, U. / Balbach, J.
CitationJournal: Biochemistry / Year: 2009
Title: Structure-Based Stability Analysis of an Extremely Stable Dimeric DNA Binding Protein from Sulfolobus islandicus
Authors: Weininger, U. / Zeeb, M. / Neumann, P. / Low, C. / Stubbs, M.T. / Lipps, G. / Balbach, J.
History
DepositionOct 15, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein ORF56
B: Uncharacterized protein ORF56


Theoretical massNumber of molelcules
Total (without water)13,0732
Polymers13,0732
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein ORF56


Mass: 6536.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (archaea) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q54323

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1712D 1H-1H NOESY
1812D 1H-1H TOCSY

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Sample preparation

DetailsContents: 1mM [U-13C; U-15N] protein, 2mM protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein_1[U-13C; U-15N]1
2 mMprotein_21
Sample conditionsIonic strength: 0.05 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker DRXBrukerDRX4002

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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