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Yorodumi- PDB-3sit: Crystal structure of porcine CRW-8 Rotavirus VP8* in complex with... -
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-Basic information
Entry | Database: PDB / ID: 3sit | |||||||||
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Title | Crystal structure of porcine CRW-8 Rotavirus VP8* in complex with aceramido-GM3 | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | SUGAR BINDING PROTEIN / VIRAL PROTEIN / beta sandwich / lectin / GM3 | |||||||||
Function / homology | Function and homology information host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane Similarity search - Function | |||||||||
Biological species | Porcine rotavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Blanchard, H. / Yu, X. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Novel structural insights into rotavirus recognition of ganglioside glycan receptors. Authors: Yu, X. / Coulson, B.S. / Fleming, F.E. / Dyason, J.C. / von Itzstein, M. / Blanchard, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sit.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sit.ent.gz | 66.9 KB | Display | PDB format |
PDBx/mmJSON format | 3sit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/3sit ftp://data.pdbj.org/pub/pdb/validation_reports/si/3sit | HTTPS FTP |
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-Related structure data
Related structure data | 3sisC 2i2sS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18459.516 Da / Num. of mol.: 2 / Fragment: Outer capsid protein VP8* (UNP residues 64-224) / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine rotavirus / Strain: CRW-8 / Plasmid: p-GEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C6Y8 #2: Polysaccharide | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15-20 mg/mL protein, 65-75% MPD, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→57.35 Å / Num. obs: 35062 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.29 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7.33 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2I2S Resolution: 1.8→40.35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.389 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.128 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.266 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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