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- PDB-1lr1: Solution Structure of the Oligomerization Domain of the Bacterial... -

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Basic information

Entry
Database: PDB / ID: 1lr1
TitleSolution Structure of the Oligomerization Domain of the Bacterial Chromatin-Structuring Protein H-NS
Componentsdna-binding protein h-ns
KeywordsDNA BINDING PROTEIN / chromatin / coiled-coil / dna packaging / nucleoid assembly
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 / dynamical simulated annealing
AuthorsEsposito, D. / Petrovic, A. / Harris, R. / Ono, S. / Eccleston, J. / Mbabaali, A. / Haq, I. / Higgins, C.F. / Hinton, J.C.D. / Driscoll, P.C. / Ladbury, J.E.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: H-NS Oligomerization Domain Structure Reveals the Mechanism for High Order Self-association of the Intact Protein
Authors: Esposito, D. / Petrovic, A. / Harris, R. / Ono, S. / Eccleston, J. / Mbabaali, A. / Haq, I. / Higgins, C.F. / Hinton, J.C. / Driscoll, P.C. / Ladbury, J.E.
History
DepositionMay 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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
B: dna-binding protein h-ns


Theoretical massNumber of molelcules
Total (without water)14,0402
Polymers14,0402
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein dna-binding protein h-ns / histone-like protein hlp-ii / protein h1 / protein b1


Mass: 7019.901 Da / Num. of mol.: 2 / Fragment: n-terminal domain (residues 1-57) / Mutation: c20s
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hns / Plasmid: pet14b / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(lambda de3) / References: UniProt: P0ACF8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 13CF1-filtered, F3-edited NOESY-HSQC
NMR detailsText: Assignment was accomplished by using standard triple resonance techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
115N labelled300 mM NaCl,20 mM potassium phosphate, 1 mM EDTA, at pH 7.0
215N,13C labelled300 mM NaCl,20 mM potassium phosphate, 1 mM EDTA, at pH 7.0
314N,12C/15N,13C 1:1 mixed labelled chains300 mM NaCl,20 mM potassium phosphate, 1 mM EDTA, at pH 7.0
Sample conditionsIonic strength: 300 mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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 UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
Azara2.6Boucher, W.processing
ANSIG3.3Kraulis, P.data analysis
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: dynamical simulated annealing / Software ordinal: 1
Details: The calculations were carried out using the PARALLHDGv5.1 parameter, with the non-bonded energy function of PROLSQ, modified to allow floating stereochemistry of prochiral centers
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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