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Yorodumi- PDB-2fmh: Crystal structure of Mg2+ and BeF3- bound CheY in complex with Ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fmh | ||||||
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Title | Crystal structure of Mg2+ and BeF3- bound CheY in complex with CheZ 200-214 solved from a F432 crystal grown in Tris (pH 8.4) | ||||||
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: 2.001 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 | 2fmh.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fmh.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/2fmh ftp://data.pdbj.org/pub/pdb/validation_reports/fm/2fmh | HTTPS FTP |
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-Related structure data
Related structure data | 2fkaC 2flkC 2flwC 2fmfC 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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2 |
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3 |
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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 , 6 types, 58 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-BEF / |
#6: Chemical | ChemComp-TRS / |
#7: Chemical | ChemComp-GOL / |
#8: 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: 8.4 Details: 2M ammonium sulfate, 0.2M lithium sulfate, 0.1M Tris, pH 8.4, 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: 1.0718 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.0718 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 22923 / Rmerge(I) obs: 0.068 / Χ2: 1.065 / D res high: 2 Å / D res low: 30 Å / % possible obs: 99.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2→30 Å / Num. all: 22957 / Num. obs: 22923 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.9 Å2 / Rsym value: 0.068 / Χ2: 1.065 / Net I/σ(I): 35.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 7 / Num. unique all: 2207 / Rsym value: 0.377 / Χ2: 1.164 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FQW Resolution: 2.001→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.601 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.762 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20
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