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Yorodumi- PDB-7c5z: Crystal structure of spring viremia of carp virus phosphoprotein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c5z | ||||||||||||
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Title | Crystal structure of spring viremia of carp virus phosphoprotein central domain | ||||||||||||
Components | Phosphoprotein | ||||||||||||
Keywords | VIRAL PROTEIN / SVCV / P protein / Central domain / dimer | ||||||||||||
Function / homology | Phosphoprotein, C-terminal domain, viral / virion component => GO:0044423 / host cell cytoplasm / cytoplasm / Phosphoprotein Function and homology information | ||||||||||||
Biological species | Spring viremia of carp virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||||||||
Authors | Wang, Z.X. / Guan, H.X. / Ouyang, S.Y. / Zhang, Y.A. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J.Virol. / Year: 2020 Title: Structural and Functional Characterization of the Phosphoprotein Central Domain of Spring Viremia of Carp Virus. Authors: Wang, Z.X. / Liu, S.B. / Guan, H. / Lu, L.F. / Tu, J.G. / Ouyang, S. / Zhang, Y.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c5z.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c5z.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 7c5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/7c5z ftp://data.pdbj.org/pub/pdb/validation_reports/c5/7c5z | HTTPS FTP |
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-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: 9768.437 Da / Num. of mol.: 2 / Fragment: central domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Spring viremia of carp virus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7J936 #2: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.4 Å3/Da / Density % sol: 48.7 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Ammonium acetate, 0.1 M Bis-Tris pH 5.5, 17% PEG 10000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→34.93 Å / Num. obs: 30365 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 22.56 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.5→1.54 Å / Num. unique obs: 2184 / CC1/2: 0.673 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→34.92 Å / SU ML: 0.1747 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.939 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: 30.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→34.92 Å
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Refine LS restraints |
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LS refinement shell |
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