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Yorodumi- PDB-5g4b: Crystal structure of Aura virus capsid protein in complex with pi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g4b | ||||||
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Title | Crystal structure of Aura virus capsid protein in complex with piperazine. | ||||||
Components | CAPSID PROTEINCapsid | ||||||
Keywords | HYDROLASE / AURA VIRUS / CAPSID / PROTEIN / PIPERAZINE | ||||||
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 / structural molecule activity / virion attachment to host cell ...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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | ||||||
Biological species | AURA VIRUS | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Aggarwal, M. / Kumar, P. / Tomar, S. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Capsid Protein from Aura Virus in Complex with Piperazine Authors: Aggarwal, M. / Kumar, P. / Tomar, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g4b.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g4b.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 5g4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/5g4b ftp://data.pdbj.org/pub/pdb/validation_reports/g4/5g4b | HTTPS FTP |
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-Related structure data
Related structure data | 4agkS 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: 17008.246 Da / Num. of mol.: 1 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-PZE / |
#3: Water | ChemComp-HOH / |
Sequence details | SOME RESIDUES ARE DIFFERENT IN OUR SEQUENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.07 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M BIS-TRIS AND 22 % POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000, pH 6.5 |
-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: Oct 31, 2013 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 4847 / % possible obs: 79.6 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.21→2.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2 / % possible all: 41.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AGK Resolution: 2.24→48.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.89 / SU B: 10.151 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 110-115 ARE DISORDERED.
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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: 38.281 Å2
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Refinement step | Cycle: LAST / Resolution: 2.24→48.11 Å
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