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- PDB-5yrc: Crystal Structure of Oxidized Cypovirus Polyhedra R13A/E73C/Y83C ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yrc | |||||||||
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Title | Crystal Structure of Oxidized Cypovirus Polyhedra R13A/E73C/Y83C Mutant | |||||||||
![]() | Polyhedrin | |||||||||
![]() | VIRAL PROTEIN / In vivo protein crystal / polyhedra / disulfide bond | |||||||||
Function / homology | Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / Polyhedrin![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Negishi, H. / Abe, S. / Yamashita, K. / Hirata, K. / Niwase, K. / Boudes, M. / Coulibaly, F. / Mori, H. / Ueno, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Supramolecular protein cages constructed from a crystalline protein matrix Authors: Negishi, H. / Abe, S. / Yamashita, K. / Hirata, K. / Niwase, K. / Boudes, M. / Coulibaly, F. / Mori, H. / Ueno, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.9 KB | Display | ![]() |
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PDB format | ![]() | 48.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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: 28320.355 Da / Num. of mol.: 1 / Mutation: R13A,E73C,Y83C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 24.99 % |
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Crystal grow | Temperature: 300 K / Method: in cell Details: In vivo crystallization in the cytoplasm of the cell, temperature 300 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→36.66 Å / Num. obs: 19524 / % possible obs: 100 % / Redundancy: 60.5 % / Net I/σ(I): 11.24 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.275 Å2
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Refinement step | Cycle: 1 / Resolution: 1.67→36.66 Å
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Refine LS restraints |
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