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Yorodumi- PDB-6wj4: The crystal structure of the 2009/H1N1/California PA endonuclease... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wj4 | ||||||
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Title | The crystal structure of the 2009/H1N1/California PA endonuclease wild type in complex with SJ000986448 | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | VIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Cuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wj4.cif.gz | 95.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wj4.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wj4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6wj4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6wj4_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 6wj4_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/6wj4 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/6wj4 | HTTPS FTP |
-Related structure data
Related structure data | 6v6xC 6v9eC 6vbrC 6vg9C 6vivC 6vjhC 6vl3C 6wijC 7k87C 7lm4C 7lw6C 7m0nC 7mpfC 7mtyC 7n47C 7n55C 7n68C 7n8fC 7rkpC 7umrC 7uuhC 8dipC 8dpjC 8dtwC 8e4sC 5vptS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23148.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus, (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1)) Gene: PA-X, PA / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A481PFF5, UniProt: C6H0Y9 |
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-Non-polymers , 5 types, 35 molecules
#2: Chemical | #3: Chemical | ChemComp-U3A / | #4: Chemical | ChemComp-QQ4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.52 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.7 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→74.44 Å / Num. obs: 9099 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 55.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.065 / Χ2: 0.4 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.55→2.66 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1072 / CC1/2: 0.879 / Rpim(I) all: 0.329 / Rrim(I) all: 0.911 / Χ2: 0.38 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vpt Resolution: 2.55→63.7 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.57 Å2 / Biso mean: 82.2965 Å2 / Biso min: 41.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→63.7 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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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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