+Open data
-Basic information
Entry | Database: PDB / ID: 5vx4 | |||||||||
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Title | VP8* of a G2P[4] Human Rotavirus | |||||||||
Components | Outer capsid protein VP4 | |||||||||
Keywords | VIRAL PROTEIN / Glycan / HBGA / rotavirus | |||||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / host cell membrane / viral capsid / symbiont entry into host cell / virion attachment to host cell / membrane Similarity search - Function | |||||||||
Biological species | Rotavirus A | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Hu, L. / Venkataram Prasad, B.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Glycan recognition in globally dominant human rotaviruses. Authors: Hu, L. / Sankaran, B. / Laucirica, D.R. / Patil, K. / Salmen, W. / Ferreon, A.C.M. / Tsoi, P.S. / Lasanajak, Y. / Smith, D.F. / Ramani, S. / Atmar, R.L. / Estes, M.K. / Ferreon, J.C. / Prasad, B.V.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vx4.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vx4.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/5vx4 ftp://data.pdbj.org/pub/pdb/validation_reports/vx/5vx4 | HTTPS FTP |
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-Related structure data
Related structure data | 5vx5C 5vx8C 5vx9C 2aenS 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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Unit cell |
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-Components
#1: Protein | Mass: 18498.297 Da / Num. of mol.: 1 / Fragment: UNP residues 54-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2VE61 |
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#2: Chemical | ChemComp-TRS / |
#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: 1.96 Å3/Da / Density % sol: 37.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M Bis-Tris propane, pH 9.0, 30% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2015 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→31.11 Å / Num. obs: 19627 / % possible obs: 94.46 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.02462 / Rpim(I) all: 0.025 / Rrim(I) all: 0.02462 / Net I/σ(I): 18.61 |
Reflection shell | Highest resolution: 1.55 Å / Rmerge(I) obs: 0.228 / CC1/2: 0.954 / Rpim(I) all: 0.122 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2AEN Resolution: 1.55→31.11 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 20.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→31.11 Å
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Refine LS restraints |
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LS refinement shell |
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