+Open data
-Basic information
Entry | Database: PDB / ID: 7f5f | ||||||
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Title | SARS-CoV-2 ORF8 S84 | ||||||
Components | ORF8 protein | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 / ORF8 | ||||||
Function / homology | Non-structural protein ORF8, betacoronavirus / ORF8, SARS-CoV-2 / Betacoronavirus NS8 protein / ORF8 protein Function and homology information | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Chen, S. / Zhou, Z. / Chen, X. | ||||||
Citation | Journal: Front Immunol / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f5f.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f5f.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 7f5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f5f_validation.pdf.gz | 410.4 KB | Display | wwPDB validaton report |
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Full document | 7f5f_full_validation.pdf.gz | 410.7 KB | Display | |
Data in XML | 7f5f_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | 7f5f_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/7f5f ftp://data.pdbj.org/pub/pdb/validation_reports/f5/7f5f | HTTPS FTP |
-Related structure data
Related structure data | 7f8lC 7jtlS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11925.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: orf8, ORF8 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B9VKN0 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 39.21 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: PEG6000, Citric acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.6195→26.55 Å / Num. obs: 13144 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 24.1878885817 Å2 / CC1/2: 1 / Net I/σ(I): 58.9 |
Reflection shell | Resolution: 1.6195→1.62 Å / Num. unique obs: 1300 / CC1/2: 0.872 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7jtl Resolution: 1.62→26.5457179551 Å / SU ML: 0.159723163904 / Cross valid method: FREE R-VALUE / σ(F): 1.36887927139 / Phase error: 20.1594548253 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 30.9362368328 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.62→26.5457179551 Å
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Refine LS restraints |
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LS refinement shell |
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