+Open data
-Basic information
Entry | Database: PDB / ID: 6oai | |||||||||
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Title | Crystal structure of P[6] rotavirus vp8* complexed with LNFPI | |||||||||
Components | Protease-sensitive outer capsid protein | |||||||||
Keywords | VIRUS / Rotavirus / host receptor interaction | |||||||||
Function / homology | Function and homology information host cell endoplasmic reticulum / peptidase activity / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / proteolysis / membrane Similarity search - Function | |||||||||
Biological species | Human rotavirus A | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Xu, S. / Liu, Y. / Jiang, X. / Kennedy, M.A. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2020 Title: Molecular basis of P[II] major human rotavirus VP8* domain recognition of histo-blood group antigens. Authors: Xu, S. / Ahmed, L.U. / Stuckert, M.R. / McGinnis, K.R. / Liu, Y. / Tan, M. / Huang, P. / Zhong, W. / Zhao, D. / 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 | 6oai.cif.gz | 145 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oai.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 6oai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oai_validation.pdf.gz | 774.8 KB | Display | wwPDB validaton report |
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Full document | 6oai_full_validation.pdf.gz | 781.4 KB | Display | |
Data in XML | 6oai_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 6oai_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/6oai ftp://data.pdbj.org/pub/pdb/validation_reports/oa/6oai | HTTPS FTP |
-Related structure data
Related structure data | 6niwSC 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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3 |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 18443.498 Da / Num. of mol.: 4 / Fragment: VP8* domain, residues 49-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rotavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: D2DXN5 #2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: 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: 2.18 Å3/Da / Density % sol: 43.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate, 1.0 M Lithium sulfate monohydrate |
-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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 1, 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: 1.9→74.89 Å / Num. obs: 48808 / % possible obs: 97.3 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Net I/σ(I): 12.4 / Num. measured all: 164606 | ||||||||||||||||||||||||
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: 1.9→45.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.182 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.166 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.03 Å2 / Biso mean: 19.793 Å2 / Biso min: 4.2 Å2
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Refinement step | Cycle: final / Resolution: 1.9→45.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.898→1.948 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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