+Open data
-Basic information
Entry | Database: PDB / ID: 3pum | ||||||
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Title | Crystal structure of P domain dimer of Norovirus VA207 | ||||||
Components | Capsid | ||||||
Keywords | VIRAL PROTEIN / Greek Key / Mixed alpha/beta Structure / Receptor Binding / Carbohydrate/Sugar Binding / Capsid | ||||||
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 | Human calicivirus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.252 Å | ||||||
Authors | Chen, Y. / Tan, M. / Xia, M. / Hao, N. / Zhang, X.C. / Huang, P. / Jiang, X. / Li, X. / Rao, Z. | ||||||
Citation | Journal: Plos Pathog. / Year: 2011 Title: Crystallography of a Lewis-binding norovirus, elucidation of strain-specificity to the polymorphic human histo-blood group antigens Authors: Chen, Y. / Tan, M. / Xia, M. / Hao, N. / Zhang, X.C. / Huang, P. / 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 | 3pum.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pum.ent.gz | 103.2 KB | Display | PDB format |
PDBx/mmJSON format | 3pum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/3pum ftp://data.pdbj.org/pub/pdb/validation_reports/pu/3pum | HTTPS FTP |
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-Related structure data
Related structure data | 3punC 3pvdC 2obtS C: citing same article (ref.) S: Starting model for refinement |
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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: 34674.652 Da / Num. of mol.: 2 / Fragment: P DOMAIN, UNP residues 222-537 / Mutation: T289N, N374D, R425G, Q466R, V482A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human calicivirus / Strain: VA97207 / Gene: CAPSID / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91H09 #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: 2.17 Å3/Da / Density % sol: 43.27 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 12% (w/v) PEG 3350, 50mM magnesium formate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 22, 2007 / Details: Rigaku Osmic Varimax Confocal optics | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rigaku Osmic Varimax Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→50 Å / Num. obs: 27339 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.771 / Net I/σ(I): 15.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OBT Resolution: 2.252→23.096 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.76 / σ(F): 0.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.592 Å2 / ksol: 0.339 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.21 Å2 / Biso mean: 32.3257 Å2 / Biso min: 14.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.252→23.096 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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