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Yorodumi- PDB-1ov9: Crystal structure of the N-terminal dimerisation domain of VicH, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ov9 | ||||||
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Title | Crystal structure of the N-terminal dimerisation domain of VicH, the H-NS protein from Vibrio cholerae | ||||||
Components | VicH protein | ||||||
Keywords | DNA BINDING PROTEIN / dimer / helix / coiled-coil | ||||||
Function / homology | Function and homology information : / chromosome organization => GO:0051276 / pilus assembly / bent DNA binding / nucleoid / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / : / protein-DNA complex / chromosome ...: / chromosome organization => GO:0051276 / pilus assembly / bent DNA binding / nucleoid / DNA-binding transcription repressor activity / minor groove of adenine-thymine-rich DNA binding / : / protein-DNA complex / chromosome / protein dimerization activity / transcription cis-regulatory region binding / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cerdan, R. / Bloch, V. / Arold, S.T. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ov9.cif.gz | 29.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ov9.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 1ov9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/1ov9 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/1ov9 | HTTPS FTP |
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-Related structure data
Related structure data | 1ni8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | the biological assembly is the dimer of the asymmetric unit. |
-Components
#1: Protein/peptide | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 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
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Displacement parameters | Biso mean: 50 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.39 Å
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Refine LS restraints | *PLUS Type: c_angle_d / Dev ideal: 1.4 |