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- PDB-8edz: The crystal structure of I38T mutant PA endonuclease (2009/H1N1/C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8edz | ||||||
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Title | The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ000986319 | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | VIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuypers, M.G. / Slavish, J.P. / Jayaraman, S. / Rankovic, Z. / White, S.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ000986319 Authors: Cuypers, M.G. / Slavish, J.P. / Rankovic, Z. / White, S.W. #1: ![]() Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential. Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / 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 | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 69.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5vptS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 25 molecules ![](data/chem/img/WFW.gif)
![](data/chem/img/QQ4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QQ4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-WFW / | ||||
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#3: Chemical | ChemComp-QQ4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→74.23 Å / Num. obs: 7865 / % possible obs: 97.4 % / Redundancy: 6 % / Biso Wilson estimate: 75.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.65→2.78 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1032 / CC1/2: 0.798 / Rpim(I) all: 0.355 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5vpt Resolution: 2.65→31.71 Å / SU ML: 0.3803 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8967 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→31.71 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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