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Open data
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Basic information
Entry | Database: PDB / ID: 6y5z | ||||||
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Title | Structure of apo Human Polyomavirus 12 VP1 | ||||||
![]() | Capsid protein VP1 | ||||||
![]() | VIRAL PROTEIN / Major Capsid Protein / Polyomavirus | ||||||
Function / homology | Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / T=7 icosahedral viral capsid / virion attachment to host cell / structural molecule activity / Capsid protein VP1![]() | ||||||
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 | ![]() | 308.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.5 KB | Display | ![]() |
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Full document | ![]() | 476 KB | Display | |
Data in XML | ![]() | 63.2 KB | Display | |
Data in CIF | ![]() | 94.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y5xC ![]() 6y5yC ![]() 6y60C ![]() 6y61C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 30708.664 Da / Num. of mol.: 5 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: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Tacsimate, 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: Apr 30, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.549→44.05 Å / Num. obs: 181696 / % possible obs: 95.31 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.35 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.056 / Net I/σ(I): 16.44 |
Reflection shell | Resolution: 1.549→1.64 Å / Mean I/σ(I) obs: 2.89 / Num. unique obs: 28058 / CC1/2: 0.855 / Rrim(I) all: 0.456 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FMG Resolution: 1.549→44.047 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.163 / WRfactor Rwork: 0.138 / SU B: 1.309 / SU ML: 0.046 / Average fsc free: 0.9501 / Average fsc work: 0.9559 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.07 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.014 Å2
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Refinement step | Cycle: LAST / Resolution: 1.549→44.047 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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