+Open data
-Basic information
Entry | Database: PDB / ID: 2obr | ||||||
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Title | Crystal Structures of P Domain of Norovirus VA387 | ||||||
Components | Capsid protein | ||||||
Keywords | VIRAL PROTEIN / Crystal Structures / P Domain / Norovirus VA387 | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cao, S. / Lou, Z. / Jiang, X. / Zhang, X.C. / Li, X. / Rao, Z. | ||||||
Citation | Journal: J.Virol. / Year: 2007 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2obr.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2obr.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 2obr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2obr_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 2obr_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 2obr_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2obr_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/2obr ftp://data.pdbj.org/pub/pdb/validation_reports/ob/2obr | HTTPS FTP |
-Related structure data
Related structure data | 2obsC 2obtC 1ihmS 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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-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.) Norovirus / Genus: Norovirus / Strain: VA387 / Plasmid: pgex-4t-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q913Z3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2006 / Details: Osmic Mirror |
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: 2.2→50 Å / Num. all: 15535 / Num. obs: 14625 / % possible obs: 95 % / Observed criterion σ(F): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.075 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.376 / Num. unique all: 1302 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ihm Resolution: 2.2→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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