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- PDB-7xhr: Crystal structure of Wild Type Cypovirus Polyhedra produced by ce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xhr | ||||||||||||
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Title | Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis | ||||||||||||
![]() | Polyhedrin | ||||||||||||
![]() | VIRAL PROTEIN / cell-free crystallization / in cell crystal | ||||||||||||
Function / homology | Cypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / viral occlusion body / host cell cytoplasm / ACETYL GROUP / Polyhedrin![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Abe, S. / Tanaka, J. / Kojima, M. / Hirata, K. / Yamashita, K. / Ueno, T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cell-free protein crystallization for nanocrystal structure determination. Authors: Abe, S. / Tanaka, J. / Kojima, M. / Kanamaru, S. / Hirata, K. / Yamashita, K. / Kobayashi, A. / 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 | ![]() | 70.4 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.6 KB | Display | ![]() |
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Full document | ![]() | 422.6 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xhsC ![]() 7xwsC ![]() 5gqmS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 28361.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ACE / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.63 Å3/Da / Density % sol: 24.73 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / Details: cell-free crystallization |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 17297 / % possible obs: 100 % / Redundancy: 399 % / CC1/2: 0.9899 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 1.8→1.81 Å / Mean I/σ(I) obs: 1.53 / Num. unique obs: 414 / CC1/2: 0.5326 |
Serial crystallography sample delivery | Method: fixed target |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5gqm Resolution: 1.801→42.299 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.227 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.128
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.194 Å2
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Refinement step | Cycle: LAST / Resolution: 1.801→42.299 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %
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