+Open data
-Basic information
Entry | Database: PDB / ID: 3h1f | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of CheY mutant D53A of Helicobacter pylori | ||||||
Components | Chemotaxis protein cheY homolog | ||||||
Keywords | SIGNALING PROTEIN / chemotaxis / sulfate-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: 2.2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3h1f.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3h1f.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 3h1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/3h1f ftp://data.pdbj.org/pub/pdb/validation_reports/h1/3h1f | HTTPS FTP |
---|
-Related structure data
Related structure data | 3gwgSC 3h1eC 3h1gC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14300.582 Da / Num. of mol.: 1 / Mutation: D53A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: CheY1 / Plasmid: pgex-6-2 / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 / References: UniProt: P71403 | ||
---|---|---|---|
#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.778048 Å3/Da / Density % sol: 30.823023 % |
---|---|
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, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 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→36.88 Å / Num. obs: 4993 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.78 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.82 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.5 / % possible all: 97 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GWG Resolution: 2.2→15.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.138 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.532 / ESU R Free: 0.244 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 14.961 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15.53 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
|