+Open data
-Basic information
Entry | Database: PDB / ID: 8rt0 | ||||||
---|---|---|---|---|---|---|---|
Title | BTV-15 VP5 pH 6.0 | ||||||
Components | Outer capsid protein VP5 | ||||||
Keywords | VIRAL PROTEIN / Bluetongue 15 VP5 Outer capsid protein pH 6.0 | ||||||
Function / homology | Outer capsid protein VP5, Orbivirus / Orbivirus outer capsid protein VP5 / viral capsid / structural molecule activity / Outer capsid protein VP5 Function and homology information | ||||||
Biological species | Bluetongue virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Stuart, D.I. / Sutton, G.C. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: J.Gen.Virol. / Year: 2024 Title: The effect of pH on the structure of Bluetongue virus VP5. Authors: Zhang, H. / El Omari, K. / Sutton, G. / Stuart, D.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8rt0.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8rt0.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rt0_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8rt0_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 8rt0_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 8rt0_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/8rt0 ftp://data.pdbj.org/pub/pdb/validation_reports/rt/8rt0 | HTTPS FTP |
-Related structure data
Related structure data | 8rt1C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 55221.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bluetongue virus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4J9Y2 |
---|---|
#2: Chemical | ChemComp-EDO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.63 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1M Sodium Chloride, 0.1M Tris, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96864 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→51.8 Å / Num. obs: 18479 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 55.96 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.19→2.25 Å / Num. unique obs: 1322 / CC1/2: 0.65 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→51.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.919 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.066 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.19→51.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|