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Yorodumi- PDB-2r18: Structural insights into the multifunctional protein VP3 of Birna... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r18 | ||||||
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Title | Structural insights into the multifunctional protein VP3 of Birnaviruses | ||||||
Components | Capsid assembly protein VP3 | ||||||
Keywords | VIRAL PROTEIN / helix / Capsid protein / Hydrolase / Protease / Serine protease / Virion | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Infectious bursal disease virus (Gumboro virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Casanas, A. / Navarro, A. / Ferrer-Orta, C. / Gonzalez, D. / Rodriguez, J.F. / Verdaguer, N. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structural insights into the multifunctional protein VP3 of birnaviruses. Authors: Casanas, A. / Navarro, A. / Ferrer-Orta, C. / Gonzalez, D. / Rodriguez, J.F. / Verdaguer, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r18.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r18.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 2r18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/2r18 ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r18 | 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: 15791.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus) Genus: Avibirnavirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25220 |
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#2: 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: 2.84 Å3/Da / Density % sol: 56.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.5M NaCl 0.1M Sodium Acetate pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0397, 1.04, 1.037 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→20 Å / Num. all: 7401 / Num. obs: 7401 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.077 / Χ2: 1.164 / Net I/σ(I): 11.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.917 / SU B: 14.481 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.336 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.016 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.356 Å / Total num. of bins used: 20
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