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- PDB-7f8l: Crystal structure of Bat coronavirus RaTG13 ORF8 accessory protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 7f8l | ||||||
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Title | Crystal structure of Bat coronavirus RaTG13 ORF8 accessory protein | ||||||
![]() | Nonstructural protein NS8 | ||||||
![]() | VIRAL PROTEIN / nonstructural protein / accessory protein | ||||||
Function / homology | Non-structural protein ORF8, betacoronavirus / ORF8, SARS-CoV-2 / Betacoronavirus NS8 protein / Nonstructural protein NS8![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, X. / Zhou, Z. / Chen, S. | ||||||
![]() | ![]() Title: Crystal Structures of Bat and Human Coronavirus ORF8 Protein Ig-Like Domain Provide Insights Into the Diversity of Immune Responses. Authors: Chen, X. / Zhou, Z. / Huang, C. / Zhou, Z. / Kang, S. / Huang, Z. / Jiang, G. / Hong, Z. / Chen, Q. / Yang, M. / He, S. / Liu, S. / Chen, J. / Li, K. / Li, X. / Liao, J. / Chen, J. / Chen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.7 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f5fC ![]() 7jtlS 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
#1: Protein | Mass: 12295.956 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 160 mM Calcium chloride, 80 mM Sodium HEPES pH 7.5, 23% (v/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→50 Å / Num. obs: 21199 / % possible obs: 95.89 % / Redundancy: 8.7 % / Rrim(I) all: 0.114 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.76→1.82 Å / Num. unique obs: 1327 / CC1/2: 0.762 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JTL Resolution: 1.762→36.95 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.96 Å2 / Biso mean: 27.3484 Å2 / Biso min: 5.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.762→36.95 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 17.6455 Å / Origin y: -2.9597 Å / Origin z: -14.1437 Å
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Refinement TLS group |
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