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Yorodumi- PDB-3r6j: Crystal Structure of the Capsid P Domain from Norwalk Virus Strai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r6j | ||||||
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Title | Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999 | ||||||
Components | VP1 protein | ||||||
Keywords | VIRAL PROTEIN / Norovirus / P-Domain / Capsid / Receptor / Histo Blood Group Antigen (HBGA) | ||||||
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 | Norwalk-like virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Hansman, G.S. / Biertumpfel, C. / McLellan, J.S. / Georgiev, I. / Chen, L. / Zhou, T. / Katayama, K. / Kwong, P.D. | ||||||
Citation | Journal: J.Virol. / Year: 2011 Title: Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability. Authors: Hansman, G.S. / Biertumpfel, C. / Georgiev, I. / McLellan, J.S. / Chen, L. / Zhou, T. / Katayama, K. / Kwong, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r6j.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r6j.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r6j_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 3r6j_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 3r6j_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3r6j_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/3r6j ftp://data.pdbj.org/pub/pdb/validation_reports/r6/3r6j | HTTPS FTP |
-Related structure data
Related structure data | 3onuSC 3onyC 3pa1C 3pa2C 3q38C 3q39C 3q3aC 3q6qC 3q6rC 3r6kC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33414.504 Da / Num. of mol.: 1 / Fragment: unp residues 225-525 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Norwalk-like virus / Strain: Hiroshima/1999/JP / Gene: Capsid protein / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54AD6 |
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#2: Chemical | ChemComp-EDO / |
#3: 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: 2.1 Å3/Da / Density % sol: 41.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Imidazole, 8.25% (w/v) PEG 8000, 1% (v/v) MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→24.78 Å / Num. obs: 28503 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 31.38 Å2 / Rsym value: 0.05 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.45 / Num. unique all: 2605 / Rsym value: 0.449 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ONU Resolution: 1.75→24.78 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→24.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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