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Yorodumi- PDB-7vp0: Crystal structure of P domain from norovirus GI.9 capsid protein. -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vp0 | ||||||
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Title | Crystal structure of P domain from norovirus GI.9 capsid protein. | ||||||
Components | VP1 | ||||||
Keywords | VIRAL PROTEIN / norovirus / p-domain / capsid | ||||||
Function / homology | Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / VP1 Function and homology information | ||||||
Biological species | Norovirus Hu/GI/Vancouver730/2004/CAN | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Katsura, K. / Sakai, N. / Hasegawa, K. / Kimura-Someya, T. / Shirouzu, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs Open Bio / Year: 2022 Title: Lewis fucose is a key moiety for the recognition of histo-blood group antigens by GI.9 norovirus, as revealed by structural analysis. Authors: Kimura-Someya, T. / Kato-Murayama, M. / Katsura, K. / Sakai, N. / Murayama, K. / Hanada, K. / Shirouzu, M. / Someya, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vp0.cif.gz | 167.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vp0.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vp0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/7vp0 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/7vp0 | HTTPS FTP |
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-Related structure data
Related structure data | 7vs8C 7vs9C 4rdjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33777.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus Hu/GI/Vancouver730/2004/CAN / Production host: Escherichia coli (E. coli) / References: UniProt: F2XMU3 #2: Chemical | #3: 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: 4.5 Å3/Da / Density % sol: 72.68 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.10M BICINE (pH 9), 1.70M Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.04 Å / Num. obs: 134729 / % possible obs: 98.1 % / Redundancy: 1.95 % / Biso Wilson estimate: 39.49 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.44 |
Reflection shell | Resolution: 2.1→2.23 Å / Num. unique obs: 21576 / CC1/2: 0.368 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4rdj Resolution: 2.1→48.04 Å / SU ML: 0.4276 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 34.9323 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 46.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.04 Å
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Refine LS restraints |
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LS refinement shell |
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