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- PDB-6y64: Structure of Sheep Polyomavirus VP1 in complex with 6'-Sialyllact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y64 | |||||||||
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Title | Structure of Sheep Polyomavirus VP1 in complex with 6'-Sialyllactosamine | |||||||||
![]() | Capsid protein VP1 | |||||||||
![]() | VIRAL PROTEIN / Major Capsid Protein / Polyomavirus | |||||||||
Function / homology | ![]() T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Stroh, L.J. / Rustmeier, N.H. / Stehle, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family. Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, 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 | ![]() | 1018.5 KB | Display | ![]() |
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PDB format | ![]() | 838.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 119 KB | Display | |
Data in CIF | ![]() | 175.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y5xC ![]() 6y5yC ![]() 6y5zC ![]() 6y60C ![]() 6y61C ![]() 6y63C ![]() 6y65C ![]() 6y66C ![]() 6y67C ![]() 6y6aC ![]() 6y9iC ![]() 4fmgS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 32466.500 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 3 types, 6 molecules ![](data/chem/img/SIA.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 6'-sialyl-N-acetyllactosamine | #7: Sugar | |
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-Non-polymers , 4 types, 2799 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-MG / #8: 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: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Magnesium chloride, PEG 800, TRIS |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→47.47 Å / Num. obs: 350203 / % possible obs: 96.81 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.04 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 17.78 |
Reflection shell | Resolution: 1.6→1.657 Å / Mean I/σ(I) obs: 2.94 / Num. unique obs: 34182 / CC1/2: 0.821 / Rrim(I) all: 0.727 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FMG Resolution: 1.6→47.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.052 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 18.38 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→47.47 Å
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Refine LS restraints |
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