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- PDB-2fka: Crystal structure of Mg(2+) and BeF(3)(-)-bound CheY in complex w... -
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Open data
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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) | ||||||
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![]() | SIGNALING PROTEIN / CHEMOTAXIS / BEF(3)(-)-BOUND CHEY / CHEY-CHEZ PEPTIDE COMPLEX | ||||||
Function / homology | ![]() archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum / histidine phosphotransfer kinase activity / regulation of chemotaxis / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / chemotaxis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guhaniyogi, J. / Robinson, V.L. / Stock, A.M. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45 KB | Display | ![]() |
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PDB format | ![]() | 32.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.9 KB | Display | ![]() |
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Full document | ![]() | 461.6 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2flkC ![]() 2flwC ![]() 2fmfC ![]() 2fmhC ![]() 2fmiC ![]() 2fmkC ![]() 1fqwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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 ![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/BEF.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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