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Yorodumi- PDB-7cp2: Crystal structure of the African swine fever virus core shell pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cp2 | ||||||
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Title | Crystal structure of the African swine fever virus core shell protein p15 | ||||||
Components | CP530R | ||||||
Keywords | VIRAL PROTEIN / African swine fever virus (ASFV) / p15 / trimer / VIRUS | ||||||
Function / homology | viral capsid assembly / virion component / host cell perinuclear region of cytoplasm / Polyprotein pp62 / CP530R Function and homology information | ||||||
Biological species | African swine fever virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å | ||||||
Authors | Liu, K.F. / Meng, Y.M. / Chai, Y. / Li, L.J. / Sun, H. / Gao, G.F. / Tan, S.G. / Qi, J.X. | ||||||
Citation | Journal: Biosaf Health / Year: 2021 Title: Crystal structure of the African swine fever virus core shell protein p15 Authors: Liu, K.F. / Meng, Y.M. / Chai, Y. / Li, L.J. / Sun, H. / Gao, G.F. / Tan, S.G. / Qi, J.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cp2.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cp2.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 7cp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cp2_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 7cp2_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 7cp2_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 7cp2_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/7cp2 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/7cp2 | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 17140.889 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus / Gene: CP530R, CP530R CDS, ASFV-Georgia_4-118 / Production host: Escherichia coli (E. coli) / References: UniProt: X2L313, UniProt: Q65179*PLUS #2: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03836 Å |
Detector | Type: SDMS / Detector: CMOS / Date: Nov 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03836 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. obs: 25170 / % possible obs: 98.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 28.11 Å2 / Rrim(I) all: 0.093 / Net I/σ(I): 21.02 |
Reflection shell | Resolution: 2.19→2.28 Å / Rmerge(I) obs: 0.836 / Num. unique obs: 2482 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.19→46.79 Å / SU ML: 0.2846 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.2278 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: 34.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→46.79 Å
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Refine LS restraints |
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LS refinement shell |
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