+Open data
-Basic information
Entry | Database: PDB / ID: 6niw | ||||||
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Title | Crystal structure of P[6] rotavirus | ||||||
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: 1.55 Å | ||||||
Authors | Xu, S. / Liu, Y. / Lakamp, L. / Ahmed, L. / 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 | 6niw.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6niw.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 6niw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/6niw ftp://data.pdbj.org/pub/pdb/validation_reports/ni/6niw | HTTPS FTP |
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-Related structure data
Related structure data | 6oaiC 5vx8S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 18429.471 Da / Num. of mol.: 4 / Fragment: VP8* domain, residues 48-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rotavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: D2DXN5 #2: Chemical | #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: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES sodium pH 7.5, 1.5 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: RAYONIX MX-225 / Detector: CCD / Date: Dec 6, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.55→73.84 Å / Num. obs: 87191 / % possible obs: 95.8 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 13.3 / Num. measured all: 299725 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vx8 Resolution: 1.55→73.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.455 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.095 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: 78.6 Å2 / Biso mean: 23.08 Å2 / Biso min: 12.1 Å2
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Refinement step | Cycle: final / Resolution: 1.55→73.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87
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LS refinement shell | Resolution: 1.547→1.588 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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