+Open data
-Basic information
Entry | Database: PDB / ID: 4jp1 | ||||||
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Title | Mg2+ bound structure of Vibrio Cholerae CheY3 | ||||||
Components | Chemotaxis protein CheY | ||||||
Keywords | SIGNALING PROTEIN / Response regulator / signal transduction / motor protein FliM | ||||||
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 | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Biswas, M. / Dasgupta, J. / Sen, U. | ||||||
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 | 4jp1.cif.gz | 40.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jp1.ent.gz | 27 KB | Display | PDB format |
PDBx/mmJSON format | 4jp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/4jp1 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/4jp1 | HTTPS FTP |
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-Related structure data
Related structure data | 3to5SC 4h60C 4hnqC 4hnrC 4hnsC 4lx8C 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
#1: Protein | Mass: 14010.287 Da / Num. of mol.: 1 / Fragment: Response regulator, UNP residues 6-128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: cheY-3, VC0395_A1653, VC395_2180 / Production host: Escherichia coli (E. coli) / References: UniProt: A5F6J9, UniProt: A0A0H3AMJ9*PLUS |
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#2: Chemical | ChemComp-MG / |
#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: 2.36 Å3/Da / Density % sol: 47.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 6000, 0.1M tris-Cl, pH=8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR |
Detector | Type: BRUKER SMART 2000 / Detector: CCD / Date: Jun 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 4716 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 70.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TO5 Resolution: 2.46→27.39 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1222602.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 103.182 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.46→27.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.076 / Total num. of bins used: 6
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Xplor file |
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