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- PDB-1ov9: Crystal structure of the N-terminal dimerisation domain of VicH, ... -

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Basic information

Entry
Database: PDB / ID: 1ov9
TitleCrystal structure of the N-terminal dimerisation domain of VicH, the H-NS protein from Vibrio cholerae
ComponentsVicH protein
KeywordsDNA BINDING PROTEIN / dimer / helix / coiled-coil
Function / homology
Function and homology information


bent DNA binding / nucleoid / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / protein-DNA complex / structural constituent of chromatin / transcription cis-regulatory region binding / protein dimerization activity / cytosol
Similarity search - Function
H-NS histone-like proteins / Histone-like protein H-NS / Histone-like protein H-NS, N-terminal / : / H-NS histone-like proteins, N-terminal domain / Histone-like protein H-NS, C-terminal domain superfamily / Histone-like protein H-NS, C-terminal domain / H-NS histone C-terminal domain / Domain in histone-like proteins of HNS family / Helix Hairpins ...H-NS histone-like proteins / Histone-like protein H-NS / Histone-like protein H-NS, N-terminal / : / H-NS histone-like proteins, N-terminal domain / Histone-like protein H-NS, C-terminal domain superfamily / Histone-like protein H-NS, C-terminal domain / H-NS histone C-terminal domain / Domain in histone-like proteins of HNS family / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCerdan, R. / Bloch, V. / Arold, S.T.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure of the N-terminal dimerisation domain of VicH, the H-NS-like protein of Vibrio Cholerae
Authors: Cerdan, R. / Bloch, V. / Yang, Y. / Bertin, P. / Dumas, C. / Rimsky, S. / Kochoyan, M. / Arold, S.T.
History
DepositionMar 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: VicH protein
B: VicH protein


Theoretical massNumber of molelcules
Total (without water)11,5032
Polymers11,5032
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-28 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.085, 49.192, 101.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-100-

HOH

21B-141-

HOH

Detailsthe biological assembly is the dimer of the asymmetric unit.

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Components

#1: Protein/peptide VicH protein


Mass: 5751.499 Da / Num. of mol.: 2 / Fragment: N-terminal Domain (residues 1-50)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: vich / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KSX6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium chloride, PEG 3350, potassium iodide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-HCl1droppH7.5
2300 mM1dropNaCl
320 mg/mlprotein1drop
40.2 M1reservoirKI
520 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→50.69 Å / Num. all: 3894 / Num. obs: 3894 / % possible obs: 88.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.085 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.2 / Num. unique all: 569 / Rsym value: 0.57 / % possible all: 90.8
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 90.8 % / Num. measured all: 11950 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 90.8 % / Rmerge(I) obs: 0.57

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NI8

1ni8


Resolution: 2.3→50 Å / Isotropic thermal model: isotropic / Cross valid method: Maximum likelihood / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 482 11 %Random
Rwork0.233 ---
all0.258 3894 --
obs0.258 3894 88.8 %-
Displacement parametersBiso mean: 50 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 0 47 799
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_mcbond_it2.451.5
X-RAY DIFFRACTIONc_mcangle_it3.7472
X-RAY DIFFRACTIONc_scbond_it3.9282
X-RAY DIFFRACTIONc_scangle_it5.7472.5
LS refinement shellResolution: 2.3→2.39 Å
RfactorNum. reflection% reflection
Rfree0.277 60 -
Rwork0.317 --
obs-441 90.7 %
Refine LS restraints
*PLUS
Type: c_angle_d / Dev ideal: 1.4

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