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Yorodumi- PDB-3qsq: Crystal structure of the projection domain of the human astroviru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qsq | ||||||
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Title | Crystal structure of the projection domain of the human astrovirus capsid protein | ||||||
Components | Capsid polyprotein | ||||||
Keywords | VIRAL PROTEIN / receptor binding domain / astrovirus capsid | ||||||
Function / homology | Turkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / identical protein binding / Capsid polyprotein VP90 Function and homology information | ||||||
Biological species | Human astrovirus 8 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dong, J. / Dong, L. / Mendez, E. / Tao, Y.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Crystal structure of the human astrovirus capsid spike. Authors: Dong, J. / Dong, L. / Mendez, E. / Tao, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qsq.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qsq.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/3qsq ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qsq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 27222.500 Da / Num. of mol.: 1 / Fragment: UNP residues 415-646 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human astrovirus 8 / Gene: ORF2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta 2 (DE3) / References: UniProt: Q9IFX1 |
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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: 2.07 Å3/Da / Density % sol: 40.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 28% PEG 3000, 0.1 M CHES, 0.1 M glycine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9794 Å |
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Detector | Date: Sep 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→55.7 Å / Num. obs: 21767 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.932 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→23.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 Å / Total num. of bins used: 20
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