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Yorodumi- PDB-6kim: Crystal structure of diamondback moth ryanodine receptor SPRY2 domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kim | |||||||||
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Title | Crystal structure of diamondback moth ryanodine receptor SPRY2 domain | |||||||||
Components | Ryanodine receptor | |||||||||
Keywords | TRANSPORT PROTEIN / diamondback moth / ryanodine receptor / ion channel / transport protein. | |||||||||
Function / homology | Function and homology information ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / membrane => GO:0016020 Similarity search - Function | |||||||||
Biological species | Plutella xylostella (diamondback moth) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.057 Å | |||||||||
Authors | Zhou, Y. / Lin, L. / Yuchi, Z. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of diamondback moth ryanodine receptor SPRY2 domain Authors: Zhou, Y. / Lin, L. / Yuchi, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kim.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kim.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 6kim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kim_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6kim_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6kim_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 6kim_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/6kim ftp://data.pdbj.org/pub/pdb/validation_reports/ki/6kim | HTTPS FTP |
-Related structure data
Related structure data | 4p9jS 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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Unit cell |
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-Components
#1: Protein | Mass: 20157.326 Da / Num. of mol.: 1 / Mutation: K1242A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plutella xylostella (diamondback moth) / Production host: Escherichia coli (E. coli) / References: UniProt: I3VR32 | ||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Sodium/Potassium phosphate, Ph 6.5. |
-Data collection
Diffraction | Mean temperature: 193.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jun 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.057→29.903 Å / Num. obs: 10749 / % possible obs: 98.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.057→2.1656 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 162 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4P9J Resolution: 2.057→29.903 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.62
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.52 Å2 / Biso mean: 27.2874 Å2 / Biso min: 8.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.057→29.903 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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