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Yorodumi- PDB-6vkx: Crystal structure of the carbohydrate-binding domain VP8* of huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vkx | ||||||
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Title | Crystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851 | ||||||
Components | Outer capsid protein VP4 | ||||||
Keywords | VIRAL PROTEIN / Rotavirus / host receptor interaction | ||||||
Function / homology | Function and homology information host cell membrane / viral capsid / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | Human rotavirus A | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Xu, S. / McGinnis, K.R. / Jiang, X. / Kennedy, M.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens. Authors: Xu, S. / McGinnis, K.R. / Liu, Y. / Huang, P. / Tan, M. / Stuckert, M.R. / Burnside, R.E. / Jacob, E.G. / Ni, S. / Jiang, X. / Kennedy, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vkx.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vkx.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/6vkx ftp://data.pdbj.org/pub/pdb/validation_reports/vk/6vkx | HTTPS FTP |
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-Related structure data
Related structure data | 6ut9C 7jhzC 7khuC 7ki5C 6niwS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 18402.191 Da / Num. of mol.: 3 / Fragment: VP8* domain, residues 17-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rotavirus A / Gene: VP8 / Production host: Escherichia coli (E. coli) / References: UniProt: M4VSS2, UniProt: A0A1Z1XCF6*PLUS #2: Chemical | ChemComp-PG4 / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.31 Å3/Da / Density % sol: 46.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1 M HEPES sodium pH 7.5, 2% v/v PEG 400, 2.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 6, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.71→56 Å / Num. obs: 48913 / % possible obs: 90 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.065 / Net I/σ(I): 12.7 / Num. measured all: 159999 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NIW Resolution: 1.71→32.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.687 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.36 Å2 / Biso mean: 21.764 Å2 / Biso min: 11.35 Å2
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Refinement step | Cycle: final / Resolution: 1.71→32.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.754 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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