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Yorodumi- PDB-2jhp: The structure of bluetongue virus VP4 reveals a multifunctional R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jhp | ||||||
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Title | The structure of bluetongue virus VP4 reveals a multifunctional RNA- capping production-line | ||||||
Components | VP4 CORE PROTEIN | ||||||
Keywords | VIRAL PROTEIN / VIRAL CAPPING ENZYME / CORE PROTEIN / VIRION PROTEIN VIRAL PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bluetongue virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Sutton, G. / Grimes, J.M. / Stuart, D.I. / Roy, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2007 Title: Bluetongue Virus Vp4 is an RNA-Capping Assembly Line. Authors: Sutton, G. / Grimes, J.M. / Stuart, D.I. / Roy, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jhp.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jhp.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/2jhp ftp://data.pdbj.org/pub/pdb/validation_reports/jh/2jhp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75501.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bluetongue virus (serotype 10 / American isolate) Strain: BTV-10 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07132 | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.7 Details: 100 MM IMIDAZOLE PH 8.0, 2%-8% PROPAN-2-OL, 0-250 MM NACL, 50 MM DTT, 2 MM ADOHCY, 5MG/ML VP4 CONCENTRATION, SITTING DROP. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933, 0.9792 | |||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: May 5, 2002 / Details: TORROIDAL MIRRORS | |||||||||
Radiation | Monochromator: DIAMOND(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→30 Å / Num. obs: 26662 / % possible obs: 99.9 % / Observed criterion σ(I): 1.2 / Redundancy: 24.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 26 | |||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 12 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.2 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.859 / SU B: 25.264 / SU ML: 0.277 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.684 / ESU R Free: 0.342 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES 270-276, 537-549 AND 601-610 ARE OMITTED.
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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