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Yorodumi- PDB-3rvp: Structure of the CheY-BeF3 Complex with substitutions at 59 and 8... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rvp | ||||||
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Title | Structure of the CheY-BeF3 Complex with substitutions at 59 and 89: N59D and E89K | ||||||
Components | Chemotaxis protein CheY | ||||||
Keywords | SIGNALING PROTEIN / Response regulator / two-component / signal transduction / CheY / Beta-alpha protein / Chemotaxis / CheZ CheA CheX / 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: 2.404 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 | 3rvp.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rvp.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/3rvp ftp://data.pdbj.org/pub/pdb/validation_reports/rv/3rvp | HTTPS FTP |
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-Related structure data
Related structure data | 3rvjC 3rvkC 3rvlC 3rvmC 3rvnC 3rvoC 3rvqC 3rvrC 3rvsC 1fqwS S: Starting model for refinement C: citing same article (ref.) |
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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: 14395.659 Da / Num. of mol.: 2 / Mutation: N59D, E89K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1882, cheY, JW1871 / Plasmid: pET28aCheYN59DE89K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AE67 |
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-Non-polymers , 6 types, 203 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: 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 Å3/Da / Density % sol: 69.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium Sulfate 2.6M, Tris 100mM pH 7.5, Glycerol 5% (v/v), MnCl2 20mM, BeCl2 1mM, NaF 10mM, 4.6mg/mL, 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-ID / Wavelength: 1.00882 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2010 / Details: Sagittal crystal |
Radiation | Monochromator: Sagitally Focused Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00882 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 18724 / Num. obs: 18144 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 32.82 Å2 / Rsym value: 0.079 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.57 / Num. unique all: 950 / Rsym value: 0.337 / % possible all: 70.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FQW Resolution: 2.404→44.58 Å / SU ML: 0.31 / Isotropic thermal model: Individual / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Phase error: 20.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.346 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.404→44.58 Å
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Refine LS restraints |
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LS refinement shell |
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