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Yorodumi- PDB-7x8u: Crystal structure of the N-terminal Solanaceae domain of the Sw-5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x8u | |||||||||
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Title | Crystal structure of the N-terminal Solanaceae domain of the Sw-5b NLR immune receptor | |||||||||
Components | Tospovirus resistance protein B | |||||||||
Keywords | PLANT PROTEIN / Solanaceae domain / coiled-coil / immune receptor | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Solanum lycopersicum (tomato) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å | |||||||||
Authors | Li, J. / Xin, J. / Xing, W. / Tao, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Crystal structure of the N-terminal Solanaceae domain of the Sw-5b NLR immune receptor Authors: Li, J. / Xin, J. / Xing, W. / Tao, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x8u.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x8u.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 7x8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x8u_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 7x8u_full_validation.pdf.gz | 429.8 KB | Display | |
Data in XML | 7x8u_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 7x8u_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/7x8u ftp://data.pdbj.org/pub/pdb/validation_reports/x8/7x8u | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29319.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: Sw5-b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q941Q8 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium bromide, 0.2 M potassium thiocyanate, 0.1 M Tris-HCl pH 7.8, 2.6% gamma-PGA (Na+ form, LM), 2.4% w/v PEG20000 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→40.49 Å / Num. obs: 9900 / % possible obs: 99.9 % / Redundancy: 18.5 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.76→2.91 Å / Rmerge(I) obs: 1.471 / Num. unique obs: 1438 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.89→31.4 Å / SU ML: 0.3169 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.3771 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→31.4 Å
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Refine LS restraints |
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LS refinement shell |
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