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- PDB-3asr: Crystal structure of P domain from Norovirus Funabashi258 stain i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3asr | |||||||||
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Title | Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with Lewis-a | |||||||||
![]() | Capsid protein | |||||||||
![]() | VIRAL PROTEIN / protein-sugar complex / Histo-blood group antigen / capsid protein / Lectin-like protein | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Kubota, T. / Kumagai, A. / Itoh, H. / Furukawa, S. / Narimatsu, H. / Wakita, T. / Ishii, K. / Takeda, N. / Someya, Y. / Shirato, H. | |||||||||
![]() | ![]() Title: Structural basis for the recognition of Lewis antigens by genogroup I norovirus Authors: Kubota, T. / Kumagai, A. / Ito, H. / Furukawa, S. / Someya, Y. / Takeda, N. / Ishii, K. / Wakita, T. / Narimatsu, H. / Shirato, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.6 KB | Display | ![]() |
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PDB format | ![]() | 108.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 40.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aspSC ![]() 3asqC ![]() 3assC ![]() 3astC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35259.641 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 221-541 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | #3: Chemical | #4: Chemical | ChemComp-NPO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.74 % / Mosaicity: 0.505 ° |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 4.6 Details: PEG 6000, hexanediol, pH 4.6, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 88663 / Num. obs: 87465 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rmerge(I) obs: 0.059 / Χ2: 2.033 / Net I/σ(I): 18.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3ASP Resolution: 1.6→31.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.584 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.28 Å2 / Biso mean: 27.2188 Å2 / Biso min: 15.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→31.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.597→1.639 Å / Total num. of bins used: 20
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