+Open data
-Basic information
Entry | Database: PDB / ID: 5zus | ||||||
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Title | P domain of GII.17-2014/15 | ||||||
Components | VP1 | ||||||
Keywords | VIRAL PROTEIN / capsid / protruding domain / dimer / HBGA recognition | ||||||
Function / homology | Function and homology information Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Norovirus GII.17 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chen, Y. / Li, X. | ||||||
Funding support | China, 1items
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Citation | Journal: J. Virol. / Year: 2019 Title: Structural Adaptations of Norovirus GII.17/13/21 Lineage through Two Distinct Evolutionary Paths. Authors: Qian, Y. / Song, M. / Jiang, X. / Xia, M. / Meller, J. / Tan, M. / Chen, Y. / Li, X. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zus.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zus.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zus_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 5zus_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 5zus_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 5zus_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/5zus ftp://data.pdbj.org/pub/pdb/validation_reports/zu/5zus | HTTPS FTP |
-Related structure data
Related structure data | 5zuqC 5zv5C 5zv7C 5zv9C 5zvcC 3punS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 226 - 529 / Label seq-ID: 5 - 308
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-Components
#1: Protein | Mass: 34474.414 Da / Num. of mol.: 2 / Fragment: P domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norovirus GII.17 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1C9I7R1, UniProt: A0A0E3X5I8*PLUS #2: 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: 2.26 Å3/Da / Density % sol: 45.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 11% (w/v) polyethylene glycol (PEG) 3350, 4%(v/v) Tacsimate (pH7.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 42553 / % possible obs: 97.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3 / Num. unique obs: 1868 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PUN Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.503 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 30.594 Å2
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Refinement step | Cycle: 1 / Resolution: 2→50 Å
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Refine LS restraints |
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