+Open data
-Basic information
Entry | Database: PDB / ID: 3to5 | ||||||
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Title | High resolution structure of CheY3 from Vibrio cholerae | ||||||
Components | CheY homolog | ||||||
Keywords | SIGNALING PROTEIN / alpha(5)beta(5) / Chemotaxis / FliM / Phosphorylation / Motor action | ||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / phosphorelay signal transduction system / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Dasgupta, J. / Sen, U. / Biswas, M. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Conformational Barrier of CheY3 and Inability of CheY4 to Bind FliM Control the Flagellar Motor Action in Vibrio cholerae Authors: Biswas, M. / Dey, S. / Khamrui, S. / Sen, U. / Dasgupta, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3to5.cif.gz | 43 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3to5.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 3to5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3to5_validation.pdf.gz | 427 KB | Display | wwPDB validaton report |
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Full document | 3to5_full_validation.pdf.gz | 427.9 KB | Display | |
Data in XML | 3to5_validation.xml.gz | 9 KB | Display | |
Data in CIF | 3to5_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/3to5 ftp://data.pdbj.org/pub/pdb/validation_reports/to/3to5 | HTTPS FTP |
-Related structure data
Related structure data | 4h60C 4hnqC 4hnrC 4hnsC 4jp1C 4lx8C 2cheS C: citing same article (ref.) 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
#1: Protein | Mass: 15180.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: cheY3, VC_2065 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: Q9KQD5, UniProt: Q6BBK8*PLUS |
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#2: Chemical | ChemComp-CA / |
#3: 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: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 6000, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2010 |
Radiation | Monochromator: Graphite / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 15742 / Num. obs: 14876 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.6 Å2 |
Reflection shell | Resolution: 1.65→1.75 Å / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CHE Resolution: 1.65→23.26 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1223213.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.4456 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→23.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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