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- PDB-2l93: Solution structure of the C-terminal domain of Salmonella H-NS -

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Basic information

Entry
Database: PDB / ID: 2l93
TitleSolution structure of the C-terminal domain of Salmonella H-NS
ComponentsDNA-binding protein H-NS
KeywordsDNA BINDING PROTEIN / H-NS / AT hook
Function / homology
Function and homology information


bent DNA binding / nucleoid / negative regulation of gene expression, epigenetic / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin / protein dimerization activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription ...bent DNA binding / nucleoid / negative regulation of gene expression, epigenetic / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin / protein dimerization activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Histone-like protein H-NS, C-terminal domain / H-NS DNA Binding Protein / Histone-like protein H-NS, N-terminal / Histone-like protein H-NS, C-terminal domain superfamily / Histone-like protein H-NS / Histone-like protein H-NS, C-terminal domain / H-NS histone family / Domain in histone-like proteins of HNS family / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA-binding protein H-NS
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins
Authors: Gordon, B.R.G. / Li, Y. / Cote, A. / Weirauch, M.T. / Ding, P. / Hughes, T.R. / Navarre, W.W. / Xia, B. / Liu, J.
History
DepositionJan 29, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 28, 2011Group: Database references
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_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein H-NS


Theoretical massNumber of molelcules
Total (without water)6,3931
Polymers6,3931
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-binding protein H-NS / H-NS / Histone-like protein HLP-II / Protein B1 / Protein H1


Mass: 6393.120 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 91-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A1S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 50mM [U-100% 13C; U-100% 15N] sodium phosphate; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 50 mM / Component: sodium phosphate-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.05 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmgeometry optimization
Amberrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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