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Yorodumi- PDB-6y63: Structure of Sheep Polyomavirus VP1 in complex with 3'-Sialyllact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y63 | |||||||||
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Title | Structure of Sheep Polyomavirus VP1 in complex with 3'-Sialyllactosamine | |||||||||
Components | Capsid protein VP1 | |||||||||
Keywords | VIRAL PROTEIN / Major Capsid Protein / Polyomavirus | |||||||||
Function / homology | Function and homology information T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Sheep polyomavirus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å | |||||||||
Authors | Stroh, L.J. / Rustmeier, N.H. / Stehle, T. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Mbio / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y63.cif.gz | 575.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y63.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6y63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/6y63 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/6y63 | HTTPS FTP |
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-Related structure data
Related structure data | 6y5xC 6y5yC 6y5zC 6y60C 6y61C 6y64C 6y65C 6y66C 6y67C 6y6aC 6y9iC 4fmgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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 AAABBBCCCDDDEEEFFFGGGHHHIIIJJJ
#1: Protein | Mass: 32466.500 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sheep polyomavirus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3ZCF3 |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose #5: Sugar | |
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-Non-polymers , 3 types, 2341 molecules
#3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.51 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: KSCN, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 1.651→48.81 Å / Num. obs: 322288 / % possible obs: 99.82 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rrim(I) all: 0.1012 / Net I/σ(I): 13.87 |
Reflection shell | Resolution: 1.651→1.71 Å / Mean I/σ(I) obs: 1.22 / Num. unique obs: 31681 / CC1/2: 0.471 / Rrim(I) all: 1.547 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FMG Resolution: 1.651→48.807 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.469 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.089 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: 21.746 Å2
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Refinement step | Cycle: LAST / Resolution: 1.651→48.807 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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