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- PDB-6fs8: Influenza B/Memphis/13/03 endonuclease with bound inhibitor, balo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fs8 | ||||||
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Title | Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA) | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | VIRAL PROTEIN / Influenza / endonuclease / inhibitor | ||||||
Function / homology | ![]() cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cusack, S. / Speranzini, V. | ||||||
![]() | ![]() Title: Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil. Authors: Omoto, S. / Speranzini, V. / Hashimoto, T. / Noshi, T. / Yamaguchi, H. / Kawai, M. / Kawaguchi, K. / Uehara, T. / Shishido, T. / Naito, A. / Cusack, 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 | ![]() | 96.1 KB | Display | ![]() |
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PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fs6C ![]() 6fs7C ![]() 6fs9C ![]() 6fsbC ![]() 5fmlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23518.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal linker GAMGSGMA / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q5V8Z9, Hydrolases; Acting on ester bonds #2: Chemical | #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for ...Details: Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml). Mother liquor was 0.2 M NaCl, 0.1 M Na(CH3)2AsO2 pH 6.5, 2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.254 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→59.86 Å / Num. obs: 37506 / % possible obs: 91.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.862 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB:5FML Resolution: 1.8→59.86 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.539 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.131 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.202 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→59.86 Å
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Refine LS restraints |
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