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Yorodumi- PDB-3h1e: Crystal structure of Mg(2+) and BeH(3)(-)-bound CheY of Helicobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h1e | ||||||
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Title | Crystal structure of Mg(2+) and BeH(3)(-)-bound CheY of Helicobacter pylori | ||||||
Components | Chemotaxis protein cheY homolog | ||||||
Keywords | SIGNALING PROTEIN / chemotaxis / BeF3-bound CheY / Cytoplasm / Flagellar rotation / Magnesium / Metal-binding / Phosphoprotein / Two-component regulatory system | ||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / chemotaxis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Lam, K.H. / Ling, T.K. / Au, S.W. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2010 Title: Crystal structure of activated CheY1 from Helicobacter pylori. Authors: Lam, K.H. / Ling, T.K. / Au, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h1e.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h1e.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/3h1e ftp://data.pdbj.org/pub/pdb/validation_reports/h1/3h1e | HTTPS FTP |
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-Related structure data
Related structure data | 3gwgSC 3h1fC 3h1gC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 14344.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: CheY1 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P71403 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BEF / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.778725 Å3/Da / Density % sol: 30.849339 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Sodium acetate, 35% MPEG2000, 0.05M Ammonium sulfate, 1mM Magnesium chloride, 1:10 beryllium, 1:100 sodium fluoride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 21, 2007 / Details: Mirrors |
Radiation | Monochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.32 Å / Num. obs: 4888 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.27 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 55.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.36 % / Rmerge(I) obs: 0.029 / Mean I/σ(I) obs: 39 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GWG Resolution: 2.4→33.32 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.156 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R Free: 0.291 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.273 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→33.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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