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Open data
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Basic information
Entry | Database: PDB / ID: 6y61 | ||||||
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Title | Structure of apo Sheep Polyomavirus VP1 | ||||||
![]() | 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 | ![]() | 542.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 517.8 KB | Display | ![]() |
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Full document | ![]() | 533.2 KB | Display | |
Data in XML | ![]() | 98.3 KB | Display | |
Data in CIF | ![]() | 135.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y5xC ![]() 6y5yC ![]() 6y5zC ![]() 6y60C ![]() 6y63C ![]() 6y64C ![]() 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
#1: Protein | Mass: 32466.500 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: KSCN, PEG 3350 |
-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: Aug 4, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.45→49.77 Å / Num. obs: 147085 / % possible obs: 94.81 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rrim(I) all: 0.086 / Net I/σ(I): 21.58 | ||||||||||||||||||
Reflection shell | Resolution: 2.45→2.538 Å / Mean I/σ(I) obs: 4.69 / Num. unique obs: 13659 / CC1/2: 0.929 / Rrim(I) all: 0.526 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FMG Resolution: 2.45→49.77 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.044 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.041 Details: Hydrogens have been added in their 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: 28.333 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→49.77 Å
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Refine LS restraints |
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LS refinement shell |
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