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- PDB-3rvm: Structure of the CheY-Mn2+ Complex with substitutions at 59 and 8... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3rvm | ||||||
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Title | Structure of the CheY-Mn2+ Complex with substitutions at 59 and 89: N59D and E89R | ||||||
![]() | Chemotaxis protein CheY | ||||||
![]() | SIGNALING PROTEIN / Response regulator / two-component / signal transduction / CheY / Beta-alpha protein / Chemotaxis / CheA CheX CheZ / Phosphorylation | ||||||
Function / homology | ![]() bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / histidine phosphotransfer kinase activity / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / histidine phosphotransfer kinase activity / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / phosphorelay signal transduction system / phosphorelay sensor kinase activity / acetyltransferase activity / chemotaxis / magnesium ion binding / signal transduction / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Starbird, C.A. / Immormino, R.M. / Silversmith, R.E. / Bourret, R.B. | ||||||
![]() | ![]() Title: Probing Mechanistic Similarities between Response Regulator Signaling Proteins and Haloacid Dehalogenase Phosphatases. Authors: Immormino, R.M. / Starbird, C.A. / Silversmith, R.E. / Bourret, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.2 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.1 KB | Display | ![]() |
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Full document | ![]() | 422.9 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rvjC ![]() 3rvkC ![]() 3rvlC ![]() 3rvnC ![]() 3rvoC ![]() 3rvpC ![]() 3rvqC ![]() 3rvrC ![]() 3rvsC ![]() 3chyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14423.673 Da / Num. of mol.: 1 / Mutation: N59D, E89R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: PEG 8000 26%, Na Cacodylate 100mM pH 6.0, Calcium Acetate 120mM, Glycerol 10% (v/v), 4.25 mg/mL CheY, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 27, 2011 / Details: Sagittal crystal |
Radiation | Monochromator: Sagitally Focused Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02631 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 20957 / Num. obs: 20182 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 9.29 Å2 / Rsym value: 0.042 / Net I/σ(I): 38.5 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 8.8 / Num. unique all: 1027 / Rsym value: 0.125 / % possible all: 71.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CHY Resolution: 1.45→23.51 Å / SU ML: 0.11 / Isotropic thermal model: Individual + TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 14.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.737 Å2 / ksol: 0.448 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→23.51 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.1328 Å / Origin y: 15.7336 Å / Origin z: 10.9323 Å
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Refinement TLS group | Selection details: chain a |