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Yorodumi- PDB-4agj: Crystal structure of the capsid protein (110-267) from Aura virus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4agj | ||||||
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Title | Crystal structure of the capsid protein (110-267) from Aura virus in complex with dioxane | ||||||
Components | CAPSID PROTEINCapsid | ||||||
Keywords | HYDROLASE / VIRAL PROTEIN / DIOXANE | ||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | AURA VIRUS | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Aggarwal, M. / Kumar, P. / Tomar, S. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal Structure of Aura Virus Capsid Protease and its Complex with Dioxane: New Insights Into Capsid-Glycoprotein Molecular Contacts. Authors: Aggarwal, M. / Tapas, S. / Preeti / Siwach, A. / Kumar, P. / Kuhn, R.J. / Tomar, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Crystallization, High-Resolution Data Collection and Preliminary Crystallographic Analysis of Aura Virus Capsid Protease and its Complex with Dioxane. Authors: Aggarwal, M. / Dhindwal, S. / Pratap, S. / Kuhn, R.J. / Kumar, P. / Tomar, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4agj.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4agj.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 4agj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/4agj ftp://data.pdbj.org/pub/pdb/validation_reports/ag/4agj | HTTPS FTP |
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-Related structure data
Related structure data | 4agkC 1kxaS 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: 17009.230 Da / Num. of mol.: 1 / Fragment: RESIDUES 110-267 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AURA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q86925, togavirin |
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#2: Chemical | ChemComp-DIO / |
#3: Water | ChemComp-HOH / |
Sequence details | SOME RESIDUES ARE FOUND TO BE DIFFERENT IN OUR DATA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.31 % / Description: NONE |
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Crystal grow | Details: BIS-TRIS AND POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. obs: 7989 / % possible obs: 83.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.34 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / % possible all: 33.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KXA Resolution: 1.98→48.17 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.617 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.232 / 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: 36.728 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→48.17 Å
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