[English] 日本語
Yorodumi- PDB-3olx: Structural and functional effects of substitution at position T+1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3olx | ||||||
---|---|---|---|---|---|---|---|
Title | Structural and functional effects of substitution at position T+1 in CheY: CheYA88S-BeF3-Mn complex | ||||||
Components | Chemotaxis protein CheY | ||||||
Keywords | SIGNALING PROTEIN / alpha-beta repeat / chemotaxis / two-component signaling / response regulator / CheA / 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 / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity ...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 / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Immormino, R.M. / Bourret, R.B. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: A Variable Active Site Residue Influences the Kinetics of Response Regulator Phosphorylation and Dephosphorylation. Authors: Immormino, R.M. / Silversmith, R.E. / Bourret, R.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3olx.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3olx.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 3olx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/3olx ftp://data.pdbj.org/pub/pdb/validation_reports/ol/3olx | HTTPS FTP |
---|
-Related structure data
Related structure data | 3olvC 3olwC 3olyC 3myyS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14128.332 Da / Num. of mol.: 2 / Mutation: A88S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: cheY / Plasmid: pRS3 / Production host: Escherichia coli (E. coli) / Strain (production host): K0641 RecA / References: UniProt: P0AE67 |
---|
-Non-polymers , 6 types, 316 molecules
#2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.9 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Ammonium Sulfate 2.4 M Glycerol 5% (v/v) Tris 100 mM pH 7.5-8.5 MnCl2 20mM BeCl2 1mM NaF 10mM 7.2 mg/mL CheY A88S 2-15-10 , VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2010 / Details: Sagital Crystal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. all: 28356 / Num. obs: 28021 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.86 Å2 / Rsym value: 0.116 / Net I/σ(I): 16.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3MYY Resolution: 2.1→26.879 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.276 Å2 / ksol: 0.339 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.97 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→26.879 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|