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- PDB-2obt: Crystal Structures of P Domain of Norovirus VA387 in Complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2obt | |||||||||
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Title | Crystal Structures of P Domain of Norovirus VA387 in Complex with Blood Group Trisaccharides type B | |||||||||
![]() | Capsid protein | |||||||||
![]() | VIRAL PROTEIN / Crystal Structures / P Domain / Norovirus VA387 / Blood Group Trisaccharides type B | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Cao, S. / Li, X. / Rao, Z. | |||||||||
![]() | ![]() Title: Structural Basis for the Recognition of Blood Group Trisaccharides by Norovirus Authors: Cao, S. / Lou, Z. / Tan, M. / Chen, Y. / Liu, Y. / Zhang, Z. / Zhang, X.C. / Jiang, X. / Li, X. / Rao, Z. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.5 KB | Display | ![]() |
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PDB format | ![]() | 57.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 835.7 KB | Display | ![]() |
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Full document | ![]() | 841.7 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2obrSC ![]() 2obsC 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35982.207 Da / Num. of mol.: 1 / Fragment: P Domain / Mutation: T355S,F375L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M MgAc, 8% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 20, 2006 / Details: mirrors |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20619 / Num. obs: 20238 / % possible obs: 97 % / Observed criterion σ(F): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1833 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2obr Resolution: 2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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