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- PDB-5gqi: Crystal structure of Cypovirus Polyhedra mutant with deletion of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gqi | ||||||
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Title | Crystal structure of Cypovirus Polyhedra mutant with deletion of Ala194 | ||||||
![]() | Polyhedrin | ||||||
![]() | VIRAL PROTEIN / In vivo protein crystal / Polyhedra | ||||||
Function / homology | Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / Polyhedrin![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Abe, S. / Tabe, H. / Ijiri, H. / Yamashita, K. / Hirata, K. / Mori, H. / Ueno, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.9 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5gqjC ![]() 5gqkC ![]() 5gqlC ![]() 5gqmC ![]() 5gqnC ![]() 2oh6S C: citing same article ( S: Starting model for refinement |
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Similar 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28286.211 Da / Num. of mol.: 1 / Mutation: S193G,194A deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 189 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/CTP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/CTP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-CTP / | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.6 Å3/Da / Density % sol: 23.27 % |
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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: ![]() ![]() ![]() |
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: 1.3→50 Å / Num. obs: 44467 / % possible obs: 100 % / Redundancy: 35.6 % / Net I/σ(I): 11.63 |
Reflection shell | Resolution: 1.3→1.38 Å |
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Processing
Software | Name: REFMAC / Version: 5.8.0135 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2OH6 Resolution: 1.3→41.99 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.885 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.054 / 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: 8.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→41.99 Å
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Refine LS restraints |
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