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Yorodumi- PDB-4drv: Cell attachment protein VP8* of a human rotavirus specifically in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4drv | |||||||||
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Title | Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | VIRAL PROTEIN / OTAVIRUS / CELL ATTACHMENT FACTOR / HISTO BLOOD GROUP ANTIGEN / GALECTIN-FOLD | |||||||||
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 | Rotavirus sp. | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | |||||||||
Authors | Hu, L. / Crawford, S.E. / Czako, R. / Cortes-Penfield, N.W. / Smith, D.F. / Le Pendu, J. / Estes, M.K. / Prasad, B.V.V. | |||||||||
Citation | Journal: Nature / Year: 2012 Title: Cell attachment protein VP8* of a human rotavirus specifically interacts with A-type histo-blood group antigen. Authors: Hu, L. / Crawford, S.E. / Czako, R. / Cortes-Penfield, N.W. / Smith, D.F. / Le Pendu, J. / Estes, M.K. / Prasad, B.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4drv.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4drv.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 4drv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4drv_validation.pdf.gz | 833.8 KB | Display | wwPDB validaton report |
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Full document | 4drv_full_validation.pdf.gz | 834.4 KB | Display | |
Data in XML | 4drv_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4drv_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/4drv ftp://data.pdbj.org/pub/pdb/validation_reports/dr/4drv | HTTPS FTP |
-Related structure data
Related structure data | 4drrC 4ds0C 1kqrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18567.623 Da / Num. of mol.: 1 / Fragment: UNP residues 64-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus sp. / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86169 |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.26 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: 30% PEG 1500 Sodium acetate trihydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 25, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→27.44 Å / Num. obs: 19362 / % possible obs: 99.4 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.56→1.64 Å / % possible all: 96.1 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7_650) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KQR Resolution: 1.56→27.44 Å / SU ML: 0.21 / σ(F): 1.45 / Phase error: 15.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.89 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.56→27.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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