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Yorodumi- PDB-3rvm: Structure of the CheY-Mn2+ Complex with substitutions at 59 and 8... -
+Open data
-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 | ||||||
Components | Chemotaxis protein CheY | ||||||
Keywords | SIGNALING PROTEIN / Response regulator / two-component / signal transduction / CheY / Beta-alpha protein / Chemotaxis / CheA CheX CheZ / Phosphorylation | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Starbird, C.A. / Immormino, R.M. / Silversmith, R.E. / Bourret, R.B. | ||||||
Citation | Journal: Biochemistry / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rvm.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rvm.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 3rvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rvm_validation.pdf.gz | 422.1 KB | Display | wwPDB validaton report |
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Full document | 3rvm_full_validation.pdf.gz | 422.9 KB | Display | |
Data in XML | 3rvm_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 3rvm_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/3rvm ftp://data.pdbj.org/pub/pdb/validation_reports/rv/3rvm | HTTPS FTP |
-Related structure data
Related structure data | 3rvjC 3rvkC 3rvlC 3rvnC 3rvoC 3rvpC 3rvqC 3rvrC 3rvsC 3chyS 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: 14423.673 Da / Num. of mol.: 1 / Mutation: N59D, E89R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1882, cheY, JW1871 / Plasmid: pET28aCheYN59DE89R / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AE67 |
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#2: Chemical | ChemComp-MN / |
#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: 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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.02631 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |