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Open data
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Basic information
Entry | Database: PDB / ID: 5axu | ||||||
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Title | Crystal Structure of Cypovirus Polyhedra R13A Mutant | ||||||
![]() | Polyhedrin | ||||||
![]() | STRUCTURAL PROTEIN / INTRACELLULAR CRYSTAL / NUCLEOTIDE BINDING | ||||||
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. / Ijiri, H. / Negishi, H. / Yamanaka, H. / Sasaki, K. / Hirata, K. / Mori, H. / Ueno, T. | ||||||
![]() | ![]() Title: Design of Enzyme-Encapsulated Protein Containers by In Vivo Crystal Engineering Authors: Abe, S. / Ijiri, H. / Negishi, H. / Yamanaka, H. / Sasaki, K. / Hirata, K. / 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 | ![]() | 71.4 KB | Display | ![]() |
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PDB format | ![]() | 50.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 991.1 KB | Display | ![]() |
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Full document | ![]() | 992.7 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5axvC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28301.197 Da / Num. of mol.: 1 / Mutation: R13A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 146 molecules ![](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/ATP.gif)
![](data/chem/img/CTP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / | ||
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#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | ChemComp-CTP / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.62 Å3/Da / Density % sol: 24.05 % |
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Crystal grow | Temperature: 300 K / Method: in cell / pH: 7 Details: IN VIVO CRYSTALLIZATION IN THE CYTOPLASM OF THE CELL, PH 7.0, TEMPERATURE 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 19, 2011 |
Radiation | Monochromator: LIQUID NITROGEN COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 24339 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 9.16 Å2 / Rsym value: 0.132 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OH6 Resolution: 1.6→32.64 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.552 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 9.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→32.64 Å
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Refine LS restraints |
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