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- PDB-1ni8: H-NS dimerization motif -

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Basic information

Entry
Database: PDB / ID: 1ni8
TitleH-NS dimerization motif
ComponentsDNA-binding protein H-NS
KeywordsDNA BINDING PROTEIN / dimerization / protein-DNA interaction
Function / homology
Function and homology information


H-NS-Cnu complex / H-NS complex / H-NS-Hha complex / negative regulation of single-species biofilm formation on inanimate substrate / bacterial nucleoid packaging / bent DNA binding / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin ...H-NS-Cnu complex / H-NS complex / H-NS-Hha complex / negative regulation of single-species biofilm formation on inanimate substrate / bacterial nucleoid packaging / bent DNA binding / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin / regulation of translation / transcription regulator complex / protein dimerization activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / RNA binding / membrane / identical protein binding / cytosol
Similarity search - Function
H-NS histone-like proteins / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding protein H-NS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SA annealing
AuthorsBloch, V. / Yang, Y. / Margeat, E. / Chavanieu, A. / Aug, M.T. / Robert, B. / Arold, S. / Rimsky, S. / Kochoyan, M.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The H-NS dimerisation domain defines a new fold contributing to DNA recognition
Authors: Bloch, V. / Yang, Y. / Margeat, E. / Chavanieu, A. / Auge, M.T. / Robert, B. / Arold, S. / Rimsky, S. / Kochoyan, M.
History
DepositionDec 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein H-NS
B: DNA-binding protein H-NS


Theoretical massNumber of molelcules
Total (without water)10,6722
Polymers10,6722
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)1 / -
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide DNA-binding protein H-NS / H-NS / HISTONE-LIKE PROTEIN HLP-II / Protein H1 / Protein B1


Mass: 5336.038 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-46 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hns / Plasmid: PQE30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0ACF8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
14113C filtred-12Cedited 2D-NOESY
NMR detailsText: experiments on heterolabelled 13C-12C dimer

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Sample preparation

DetailsContents: peptide 1 to 2 mM / Solvent system: 200 mM NaCl, 10 mM Phosphate, pH 6.8
Sample conditionsIonic strength: 200 mM NaCl / pH: 6.8 / Pressure: normal / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4Delsucprocessing
X-PLOR3.8Brunger, Nilgesstructure solution
X-PLOR3.8Brunger, Nilgesrefinement
RefinementMethod: SA annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformers submitted total number: 1

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