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Open data
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Basic information
Entry | Database: PDB / ID: 5deb | |||||||||
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Title | 2009 H1N1 PA endonuclease mutant E119D in complex with rUMP | |||||||||
![]() | Polymerase acidic protein | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / influenza / resistance / endonuclease inhibitor / viral protein / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Kumar, G. / White, S.W. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor. Authors: Song, M.S. / Kumar, G. / Shadrick, W.R. / Zhou, W. / Jeevan, T. / Li, Z. / Slavish, P.J. / Fabrizio, T.P. / Yoon, S.W. / Webb, T.R. / Webby, R.J. / White, S.W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.7 KB | Display | ![]() |
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PDB format | ![]() | 69 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 851 KB | Display | ![]() |
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Full document | ![]() | 851 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ccyC ![]() 5cgvC ![]() 5cl0C ![]() 5cznSC ![]() 5d2oC ![]() 5d42C ![]() 5d4gC ![]() 5d8uC ![]() 5d9jC ![]() 5dbsC ![]() 5desC 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: 23134.316 Da / Num. of mol.: 1 Fragment: endonuclease domain (UNP residues 1-50, 73-196 connected by GGS linker) Mutation: E119D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds | ||||
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#2: Chemical | #3: Chemical | ChemComp-U5P / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 1.0 M ammonium sulfate, 2% w/v PEG400, 50 mM magnesium chloride, 50 mM manganese chloride, 200 mM rUMP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2014 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00522 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. obs: 17236 / % possible obs: 99.7 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 36.82 |
Reflection shell | Resolution: 2.07→2.14 Å / Redundancy: 10.2 % / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5CZN Resolution: 2.14→46.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 142.21 Å2 / Biso mean: 68.585 Å2 / Biso min: 37.99 Å2
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Refinement step | Cycle: final / Resolution: 2.14→46.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.195 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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