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Yorodumi- PDB-5yr1: Crystal Structure of Cypovirus Polyhedra R13A/E73C/Y83C/S193C/A19... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yr1 | |||||||||
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Title | Crystal Structure of Cypovirus Polyhedra R13A/E73C/Y83C/S193C/A194C Mutant | |||||||||
Components | Polyhedrin | |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | Bombyx mori cytoplasmic polyhedrosis virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | |||||||||
Authors | Negishi, H. / Abe, S. / Yamashita, K. / Hirata, K. / Niwase, K. / Boudes, M. / Coulibaly, F. / Mori, H. / Ueno, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Chem. Commun. (Camb.) / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yr1.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yr1.ent.gz | 47.6 KB | Display | PDB format |
PDBx/mmJSON format | 5yr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yr1_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 5yr1_full_validation.pdf.gz | 440.3 KB | Display | |
Data in XML | 5yr1_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5yr1_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/5yr1 ftp://data.pdbj.org/pub/pdb/validation_reports/yr/5yr1 | HTTPS FTP |
-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: 28368.484 Da / Num. of mol.: 1 / Mutation: R13A,E73C,Y83C,S193C,A194C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori cytoplasmic polyhedrosis virus Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11041 | ||
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#2: Chemical | ChemComp-EDO / #3: 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: 1.63 Å3/Da / Density % sol: 24.66 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→32.76 Å / Num. obs: 17570 / % possible obs: 98.5 % / Redundancy: 4.9 % / Net I/σ(I): 5.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→32.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.213 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.128 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.313 Å2
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Refinement step | Cycle: 1 / Resolution: 1.72→32.76 Å
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Refine LS restraints |
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