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Yorodumi- PDB-5gqk: Crystal structure of Cypovirus Polyhedra mutant with deletion of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gqk | ||||||
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Title | Crystal structure of Cypovirus Polyhedra mutant with deletion of Gly192-Ala194 | ||||||
Components | Polyhedrin | ||||||
Keywords | VIRAL PROTEIN / In vivo protein crystal / Polyhedra | ||||||
Function / homology | Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / Polyhedrin Function and homology information | ||||||
Biological species | Bombyx mori cypovirus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Abe, S. / Tabe, H. / Ijiri, H. / Yamashita, K. / Hirata, K. / Mori, H. / Ueno, T. | ||||||
Citation | Journal: ACS Nano / Year: 2017 Title: Crystal Engineering of Self-Assembled Porous Protein Materials in Living Cells Authors: Abe, S. / Tabe, H. / Ijiri, H. / Yamashita, K. / Hirata, K. / Atsumi, K. / Shimoi, T. / Akai, M. / Mori, H. / Kitagawa, S. / Ueno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gqk.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gqk.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gqk_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 5gqk_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 5gqk_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5gqk_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/5gqk ftp://data.pdbj.org/pub/pdb/validation_reports/gq/5gqk | HTTPS FTP |
-Related structure data
Related structure data | 5gqiC 5gqjC 5gqlC 5gqmC 5gqnC 2oh6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28172.107 Da / Num. of mol.: 1 / Mutation: 192G,193S,194A deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori cypovirus 1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041 | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | ChemComp-EDO / #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: 1.61 Å3/Da / Density % sol: 23.45 % |
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Crystal grow | Temperature: 300 K / Method: in cell / Details: In vivo crystallization |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 28574 / % possible obs: 98.3 % / Redundancy: 5.6 % / Net I/σ(I): 6.06 |
Reflection shell | Resolution: 1.5→1.59 Å |
-Processing
Software | Name: REFMAC / Version: 5.8.0135 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OH6 Resolution: 1.5→41.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.92 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 8.592 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→41.97 Å
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Refine LS restraints |
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