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Yorodumi- PDB-3oly: Structural and functional effects of substitution at position T+1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oly | ||||||
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Title | Structural and functional effects of substitution at position T+1 in CheY: CheYA88M-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: 2.05 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oly.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oly.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 3oly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/3oly ftp://data.pdbj.org/pub/pdb/validation_reports/ol/3oly | HTTPS FTP |
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-Related structure data
Related structure data | 3olvC 3olwC 3olxC 3myyS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 14172.451 Da / Num. of mol.: 2 / Mutation: A88M 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 |
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-Non-polymers , 5 types, 337 molecules
#2: Chemical | #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / | #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: 4.07 Å3/Da / Density % sol: 69.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium Sulfate 2.4 M Glycerol 2.5% (v/v) Tris 100 mM pH 8.0 MnCl2 20mM BeCl2 1mM NaF 10mM 4.8 mg/mL CheY A88M 1-10-10, 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 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: 2.05→50 Å / Num. all: 30591 / Num. obs: 30464 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 35.35 Å2 / Rsym value: 0.114 / Net I/σ(I): 15.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3MYY Resolution: 2.05→26.722 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / 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: 53.447 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→26.722 Å
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Refine LS restraints |
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LS refinement shell |
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