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Yorodumi- PDB-8tn8: Crystal structure of the murine astrovirus capsid spike at 1.75 A -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tn8 | ||||||
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Title | Crystal structure of the murine astrovirus capsid spike at 1.75 A | ||||||
Components | Capsid polyprotein VP90 | ||||||
Keywords | VIRAL PROTEIN / capsid / spike / attachment / homodimer | ||||||
Function / homology | Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / Viral coat protein subunit / : / Capsid polyprotein VP90 Function and homology information | ||||||
Biological species | Murine astrovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Lanning, S. / DuBois, R.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Gen.Virol. / Year: 2023 Title: Structure and immunogenicity of the murine astrovirus capsid spike. Authors: Lanning, S. / Pedicino, N. / Haley, D.J. / Hernandez, S. / Cortez, V. / DuBois, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tn8.cif.gz | 249.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tn8.ent.gz | 178.1 KB | Display | PDB format |
PDBx/mmJSON format | 8tn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tn8_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 8tn8_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 8tn8_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 8tn8_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/8tn8 ftp://data.pdbj.org/pub/pdb/validation_reports/tn/8tn8 | 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: 29257.432 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murine astrovirus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): T7 express / References: UniProt: A0A482N9T7 #2: Chemical | #3: 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: 2.16 Å3/Da / Density % sol: 43.11 % / Description: Small rod shaped crystal |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: Potassium formate, PEG 3350 / PH range: 7.3-8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→43.76 Å / Num. obs: 46845 / % possible obs: 94.79 % / Redundancy: 1.7 % / Biso Wilson estimate: 19.93 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2226 / CC1/2: 0.936 / % possible all: 92.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.75 Å / SU ML: 0.1755 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.8905 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→43.75 Å
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Refine LS restraints |
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LS refinement shell |
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