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Yorodumi- PDB-2p3j: Crystal structure of the Arg101Ala mutant protein of Rhesus rotav... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p3j | ||||||
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Title | Crystal structure of the Arg101Ala mutant protein of Rhesus rotavirus VP8* | ||||||
Components | VP4 | ||||||
Keywords | VIRAL PROTEIN / beta-sandwich | ||||||
Function / homology | Function and homology information host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane Similarity search - Function | ||||||
Biological species | Rhesus rotavirus | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Blanchard, H. | ||||||
Citation | Journal: Glycobiology / Year: 2009 Title: Effects on sialic acid recognition of amino acid mutations in the carbohydrate-binding cleft of the rotavirus spike protein Authors: Kraschnefski, M.J. / Bugarcic, A. / Fleming, F.E. / Yu, X. / von Itzstein, M. / Coulson, B.S. / Blanchard, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p3j.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p3j.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 2p3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p3j_validation.pdf.gz | 801.1 KB | Display | wwPDB validaton report |
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Full document | 2p3j_full_validation.pdf.gz | 801 KB | Display | |
Data in XML | 2p3j_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 2p3j_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/2p3j ftp://data.pdbj.org/pub/pdb/validation_reports/p3/2p3j | HTTPS FTP |
-Related structure data
Related structure data | 2p3iC 2p3kC 1kqrS 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: 18069.947 Da / Num. of mol.: 1 / Fragment: VP8* domain (fragment 64-224) / Mutation: R101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhesus rotavirus / Species: Rotavirus A / Strain: Rhesus / Plasmid: pGEX-VP8 (64-224) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q91HI9, UniProt: P12473*PLUS |
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#2: Chemical | ChemComp-SO4 / |
#3: Sugar | ChemComp-MNA / |
#4: 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: 2.14 Å3/Da / Density % sol: 42.52 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.7M (NH4)2SO4, 2.4% v/v PEG 400, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→65 Å / Num. obs: 12064 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→2.04 Å / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1521 / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: RRV VP8* PDB code 1KQR Resolution: 1.9→45.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.871 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.146 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.025 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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