+Open data
-Basic information
Entry | Database: PDB / ID: 8ixw | ||||||
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Title | Tilapia lake virus S8 segment | ||||||
Components | Chains: A,B | ||||||
Keywords | VIRUS / Tilapia lake virus / S8 segment | ||||||
Function / homology | selenourea / Nucleocapsid protein Function and homology information | ||||||
Biological species | Tilapia lake virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Wang, Z.X. / Zhang, Y.A. / Ouyang, S.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure and function of tilapia lake virus S8 segment Authors: Wang, Z.X. / 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 | 8ixw.cif.gz | 153.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ixw.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ixw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ixw_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8ixw_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8ixw_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 8ixw_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/8ixw ftp://data.pdbj.org/pub/pdb/validation_reports/ix/8ixw | 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: 19532.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tilapia lake virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y9SHR5 #2: Chemical | ChemComp-SEY / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.83 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion Details: 0.08 M Potassium chloride, 0.02 M Barium chloride dihydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 40% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride. |
-Data collection
Diffraction | Mean temperature: 298.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20.96 Å / Num. obs: 38281 / % possible obs: 96.24 % / Redundancy: 3.6 % / Biso Wilson estimate: 26.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03903 / Rpim(I) all: 0.02444 / Rrim(I) all: 0.0462 / Net I/σ(I): 20.12 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.2111 / Num. unique obs: 3781 / CC1/2: 0.982 / Rpim(I) all: 0.1272 / Rrim(I) all: 0.2468 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→20.96 Å / SU ML: 0.1786 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 19.0587 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: 34.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20.96 Å
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Refine LS restraints |
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LS refinement shell |
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