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Yorodumi- PDB-7f0h: Structural and functional characterization of bovine G1P[5] rotav... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f0h | ||||||||||||||||||||||||||||
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Title | Structural and functional characterization of bovine G1P[5] rotavirus VP8* protein | ||||||||||||||||||||||||||||
Components | Outer capsid protein VP8*Keywords | VIRAL PROTEIN / glycan binding specificity / sialic acid / histo-blood group antigen | 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 A | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å | Authors | Duan, Z. / Sun, X. | Funding support | China, 1items |
Citation | Journal: Virology / Year: 2021 | Title: Structural and functional characterization of bovine G1P[5] rotavirus VP8* protein. Authors: Dang, L. / Su, Y. / Qi, J. / Wu, Z. / Li, D. / Wang, M. / Zhang, Q. / Wang, H. / Bai, R. / Duan, Z. / Sun, X. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f0h.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f0h.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 7f0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f0h_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 7f0h_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 7f0h_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 7f0h_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/7f0h ftp://data.pdbj.org/pub/pdb/validation_reports/f0/7f0h | HTTPS FTP |
-Related structure data
Related structure data | 5jdbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18087.424 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A / Production host: Escherichia phage Ecwhy_1 (virus) / References: UniProt: E2EA93 #2: 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: 4.76 Å3/Da / Density % sol: 74.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.5 M ammonium sulfate, 0.1 M tri-sodium citrate dihydrate pH 5.6, 1.0 M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 113 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03923 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03923 Å / Relative weight: 1 |
Reflection | Resolution: 1.695→50 Å / Num. obs: 76163 / % possible obs: 98.54 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 24.004 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.409 / Rsym value: 0.874 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JDB Resolution: 1.695→31.806 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.03 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.74 Å2 / Biso mean: 18.5166 Å2 / Biso min: 6.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.695→31.806 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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