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Yorodumi- PDB-4rdl: Crystal structure of Norovirus Boxer P domain in complex with Lew... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rdl | |||||||||
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Title | Crystal structure of Norovirus Boxer P domain in complex with Lewis y tetrasaccharide | |||||||||
Components | Capsid | |||||||||
Keywords | VIRAL PROTEIN / mixed alpha/beta structure / receptor binding / HBGA / virus 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 / Viral coat protein subunit / Beta Barrel / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | Human calicivirus NLV/Boxer/2001/US | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.449 Å | |||||||||
Authors | Hao, N. / Chen, Y. / Xia, M. / Liu, W. / Tan, M. / Jiang, X. / Li, X. | |||||||||
Citation | Journal: Protein Cell / Year: 2015 Title: Crystal structures of GI.8 Boxer virus P dimers in complex with HBGAs, a novel evolutionary path selected by the Lewis epitope. Authors: Hao, N. / Chen, Y. / Xia, M. / Tan, M. / Liu, W. / Guan, X. / 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 | 4rdl.cif.gz | 280.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rdl.ent.gz | 224.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rdl_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4rdl_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4rdl_validation.xml.gz | 31.2 KB | Display | |
Data in CIF | 4rdl_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/4rdl ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rdl | HTTPS FTP |
-Related structure data
Related structure data | 4rdjSC 4rdkC 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: 33758.879 Da / Num. of mol.: 2 / Fragment: Protrusion domain, UNP residues 227-526 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human calicivirus NLV/Boxer/2001/US / Plasmid: pGex-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8BCA3 #2: Polysaccharide | #3: 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: 2.74 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M LiCl, 18%(w/v) PEG 3350, 10%(v/v) MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2012 / Details: mirrors |
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: 1.449→50 Å / Num. all: 129481 / Num. obs: 129481 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.449→1.48 Å / Redundancy: 11 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 6.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4RDJ Resolution: 1.449→47.701 Å / SU ML: 0.14 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.399 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.449→47.701 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: 30 / % reflection obs: 100 %
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