+Open data
-Basic information
Entry | Database: PDB / ID: 3zed | ||||||
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Title | X-ray structure of the birnavirus VP1-VP3 complex | ||||||
Components |
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Keywords | VIRAL PROTEIN / VIRUS MORPHOGENESIS | ||||||
Function / homology | Function and homology information T=13 icosahedral viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral genome replication / virion component / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / structural molecule activity / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | INFECTIOUS PANCREATIC NECROSIS VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Bahar, M.W. / Sarin, L.P. / Graham, S.C. / Pang, J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Structure of a Vp1-Vp3 Complex Suggests How Birnaviruses Package the Vp1 Polymerase. Authors: Bahar, M.W. / Sarin, L.P. / Graham, S.C. / Pang, J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zed.cif.gz | 940.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zed.ent.gz | 772.7 KB | Display | PDB format |
PDBx/mmJSON format | 3zed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3zed ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3zed | HTTPS FTP |
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-Related structure data
Related structure data | 2yi9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 95632.492 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFECTIOUS PANCREATIC NECROSIS VIRUS / Strain: JASPER / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: P22173, RNA-directed RNA polymerase #2: Protein | Mass: 27244.477 Da / Num. of mol.: 3 / Fragment: VP3 C-TERMINAL PEPTIDE RESIDUES 735-972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFECTIOUS PANCREATIC NECROSIS VIRUS / Strain: JASPER / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) / References: UniProt: P05844 #3: Chemical | #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47.04 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 20% (W/V) POLYETHYLENE GLYCOL 3350 AND 0.2M POTASSIUM FLUORIDE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→68.4 Å / Num. obs: 123796 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 46.48 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.2 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YI9 Resolution: 2.2→59.13 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9392 / SU R Cruickshank DPI: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.265 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.186
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Displacement parameters | Biso mean: 55.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.308 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→59.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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