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- PDB-6gvz: GII.1 human norovirus protruding domain in complex with glycochen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gvz | ||||||
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Title | GII.1 human norovirus protruding domain in complex with glycochenodeoxycholate (GCDCA) | ||||||
![]() | Capsid protein VP1 | ||||||
![]() | VIRAL PROTEIN / Norovirus / GII.1 / P domain / GCDCA / HBGA | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kilic, T. / Hansman, G.S. | ||||||
![]() | ![]() Title: Structural Basis for Human Norovirus Capsid Binding to Bile Acids. Authors: Kilic, T. / Koromyslova, A. / Hansman, G.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.5 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 639.2 KB | Display | ![]() |
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Full document | ![]() | 639.2 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 22.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gw0C ![]() 6gw1C ![]() 6gw2C ![]() 6gw4C ![]() 4roxS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 33650.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal GPGS is part of an expression tag. / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CHO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0,1M Sodium chloride 0,005 M Magnesium chloride hexahydrate 0,1 M Tris 8,5 30 % w/v PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→59.86 Å / Num. obs: 44174 / % possible obs: 99.36 % / Redundancy: 13.7 % / Biso Wilson estimate: 16.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05719 / Rpim(I) all: 0.01599 / Rrim(I) all: 0.05943 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.54→1.59 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.6674 / Mean I/σ(I) obs: 3.57 / Num. unique obs: 4133 / CC1/2: 0.938 / Rpim(I) all: 0.1883 / Rrim(I) all: 0.694 / % possible all: 94.22 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ROX Resolution: 1.54→33.892 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→33.892 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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