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Yorodumi- PDB-2fka: Crystal structure of Mg(2+) and BeF(3)(-)-bound CheY in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fka | ||||||
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Title | Crystal structure of Mg(2+) and BeF(3)(-)-bound CheY in complex with CheZ(200-214) solved from a F432 crystal grown in CAPS (pH 10.5) | ||||||
Components |
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Keywords | SIGNALING PROTEIN / CHEMOTAXIS / BEF(3)(-)-BOUND CHEY / CHEY-CHEZ PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis / phosphoprotein phosphatase activity / phosphorelay signal transduction system / chemotaxis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Guhaniyogi, J. / Robinson, V.L. / Stock, A.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structures of Beryllium Fluoride-free and Beryllium Fluoride-bound CheY in Complex with the Conserved C-terminal Peptide of CheZ Reveal Dual Binding Modes Specific to CheY Conformation. Authors: Guhaniyogi, J. / Robinson, V.L. / Stock, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fka.cif.gz | 45 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fka.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/2fka ftp://data.pdbj.org/pub/pdb/validation_reports/fk/2fka | HTTPS FTP |
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-Related structure data
Related structure data | 2flkC 2flwC 2fmfC 2fmhC 2fmiC 2fmkC 1fqwS 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 on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 14140.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: cheY / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P0A2D5 |
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#2: Protein/peptide | Mass: 1622.687 Da / Num. of mol.: 1 / Fragment: residues 200-214 / Source method: obtained synthetically Details: This sequence corresponds to the C-terminal 15 residues of the CheZ protein occurring naturally in Salmonella enterica serovar Typhumurium References: UniProt: P07800 |
-Non-polymers , 5 types, 86 molecules
#3: Chemical | ChemComp-MG / | ||||
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#4: Chemical | ChemComp-SO4 / | ||||
#5: Chemical | #6: Chemical | ChemComp-BEF / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 2M ammonium sulfate, 0.2M lithium sulfate, 0.1M CAPS, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2003 |
Radiation | Monochromator: KOHZU double crystal monochromator with a sagittally focused second crystal. Crystal type Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 23282 / Num. obs: 23259 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.058 / Rsym value: 0.05 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 7.1 / Num. unique all: 2253 / Rsym value: 0.209 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FQW Resolution: 2→19.96 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.409 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.598 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20 /
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