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Open data
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Basic information
Entry | Database: PDB / ID: 8y6d | ||||||
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Title | Norovirus GII.10 P domain and 2'-FL (tablet) | ||||||
![]() | GII.10 norovirus P domain in complex with 2'-FL (tablet) | ||||||
![]() | VIRAL PROTEIN / Sugar / complex / milk oligosaccharide | ||||||
Function / homology | NITRATE ION / DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansman, G. / Tame, J.R.H. / Kher, G. / Pancera, M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Norovirus GII.10 P domain and 2'-FL (tablet) Authors: Hansman, G. / Tame, J.R.H. / Kher, G. / Pancera, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.1 KB | Display | ![]() |
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PDB format | ![]() | 198.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 889.9 KB | Display | ![]() |
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Full document | ![]() | 893.1 KB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 45.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 34506.660 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE GENEBANK ACCESSION NUMBER IS AF504671 FOR THIS PROTEIN. Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 609 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NO3 / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.17 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium nitrate 0.1 M bis-tris propane (pH 7.5) 20% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→43.55 Å / Num. obs: 133866 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Rrim(I) all: 0.067 / Χ2: 0.49 / Net I/σ(I): 9 / Num. measured all: 608864 |
Reflection shell | Resolution: 1.41→1.43 Å / % possible obs: 93.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 1.261 / Num. measured all: 26159 / Num. unique obs: 6219 / CC1/2: 0.506 / Rpim(I) all: 0.673 / Rrim(I) all: 1.435 / Χ2: 0.37 / Net I/σ(I) obs: 0.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→43.55 Å
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Refine LS restraints |
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LS refinement shell |
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