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- PDB-4agj: Crystal structure of the capsid protein (110-267) from Aura virus... -
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Open data
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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 | ||||||
![]() | CAPSID PROTEIN | ||||||
![]() | HYDROLASE / VIRAL PROTEIN / DIOXANE | ||||||
Function / homology | ![]() 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 / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Aggarwal, M. / Kumar, P. / Tomar, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.6 KB | Display | ![]() |
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PDB format | ![]() | 50.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442 KB | Display | ![]() |
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Full document | ![]() | 443.8 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4agkC ![]() 1kxaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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Refine LS restraints |
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