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Yorodumi- PDB-3myy: Structure of E. Coli CheY mutant A113P bound to Beryllium fluoride -
+Open data
-Basic information
Entry | Database: PDB / ID: 3myy | ||||||
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Title | Structure of E. Coli CheY mutant A113P bound to Beryllium fluoride | ||||||
Components | Chemotaxis protein cheY | ||||||
Keywords | SIGNALING PROTEIN / Chemotaxis / CheA / CheB / CheX / CheZ / two-component signaling / response regulator | ||||||
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 K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Immormino, R.M. / McDonald, L.R. / Bourret, R.B. | ||||||
Citation | Journal: To be Published Title: Activation of CheY by Mutation at an allosteric site Authors: Immormino, R.M. / McDonald, L.R. / Lee, A.L. / 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 | 3myy.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3myy.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 3myy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/3myy ftp://data.pdbj.org/pub/pdb/validation_reports/my/3myy | HTTPS FTP |
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-Related structure data
Related structure data | 1fqwS 3i66 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14007.173 Da / Num. of mol.: 2 / Fragment: CheY / Mutation: A113P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b1882, cheY, JW1871 / Plasmid: pRS3 / Production host: Escherichia coli (E. coli) / Strain (production host): K0641 RecA / References: UniProt: P0AE67 |
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-Non-polymers , 5 types, 412 molecules
#2: Chemical | ChemComp-BEF / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Ammonium Sulfate 1.8-2.4 M, Glycerol 0-12.5% (v/v), Tris 100 mM, pH 7.0-8.5, MnCl2 20mM, BeCl2 1mM, NaF 10mM, , VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 11, 2009 / Details: Osmic mirrors |
Radiation | Monochromator: Copper K alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. all: 29803 / Num. obs: 29803 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 35.6 Å2 / Rsym value: 0.138 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1449 / Rsym value: 0.628 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FQW Resolution: 2.1→27.591 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.034 Å2 / ksol: 0.376 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→27.591 Å
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Refine LS restraints |
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LS refinement shell |
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