+Open data
-Basic information
Entry | Database: PDB / ID: 6ioq | |||||||||||||||
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Title | The ligand binding domain of Mlp24 with glycine | |||||||||||||||
Components | Methyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins | |||||||||||||||
Keywords | SIGNALING PROTEIN / CHEMORECEPTOR / LIGAND COMPLEX / MCP-LIKE PROTEIN / PAS-LIKE DOMAIN | |||||||||||||||
Function / homology | Function and homology information chemotaxis / membrane => GO:0016020 / signal transduction / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 Å | |||||||||||||||
Authors | Takahashi, Y. / Sumita, K. / Nishiyama, S. / Kawagishi, I. / Imada, K. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: J. Bacteriol. / Year: 2019 Title: Calcium Ions Modulate Amino Acid Sensing of the Chemoreceptor Mlp24 ofVibrio cholerae. Authors: Takahashi, Y. / Nishiyama, S.I. / Sumita, K. / Kawagishi, I. / Imada, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ioq.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ioq.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ioq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/6ioq ftp://data.pdbj.org/pub/pdb/validation_reports/io/6ioq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28607.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: mcpB_4, ERS013206_02812 / Plasmid: pGEX 6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H6VSA0, UniProt: Q9KQ43*PLUS |
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#2: Chemical | ChemComp-GLY / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 20% (w/v) PEG 8000, 0.2M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2016 |
Radiation | Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→41.6 Å / Num. obs: 25096 / % possible obs: 98.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.14→2.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3 / Num. unique obs: 3946 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.143→41.599 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.143→41.599 Å
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Refine LS restraints |
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LS refinement shell |
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