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Open data
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Basic information
Entry | Database: PDB / ID: 5zv9 | ||||||
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Title | P domain of GII.13 norovirus capsid | ||||||
![]() | Major capsid protein VP1 | ||||||
![]() | VIRAL PROTEIN / capsid / protruding domain / dimer / HBGA recognition | ||||||
Function / homology | ![]() Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chen, Y. / Li, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Adaptations of Norovirus GII.17/13/21 Lineage through Two Distinct Evolutionary Paths. Authors: Qian, Y. / Song, M. / Jiang, X. / Xia, M. / Meller, J. / Tan, M. / Chen, Y. / Li, X. / Rao, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 266.2 KB | Display | ![]() |
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PDB format | ![]() | 215.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zuqC ![]() 5zusC ![]() 5zv5C ![]() 5zv7C ![]() 5zvcC ![]() 4rlzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34688.621 Da / Num. of mol.: 2 / Fragment: P domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M succinic acid (pH 7.0), 15% (w/v) polyethylene glycol (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 59172 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 2893 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RLZ Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.944 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.122 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.243 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→50 Å
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Refine LS restraints |
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