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Yorodumi- PDB-6v53: The crystal structure of the 2009 H1N1 PA endonuclease mutant I38... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v53 | ||||||
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Title | The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000985494 | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | VIRAL PROTEIN / NUCLEASE INFLUENZA INHIBITOR RESISTANCE / HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of the 2009 H1N1 PA endonuclease mutant I38T in complex with SJ000985494 Authors: Cuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W. #1: 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 | 6v53.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v53.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 6v53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v53_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 6v53_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 6v53_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 6v53_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/6v53 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/6v53 | HTTPS FTP |
-Related structure data
Related structure data | 6v56C 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: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1)) Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C6H0Y9 |
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-Non-polymers , 5 types, 58 molecules
#2: Chemical | ChemComp-QPY / | ||||
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#3: Chemical | ChemComp-QQ4 / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-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: 3.15 Å3/Da / Density % sol: 60.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 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 / Ambient temp details: cryostream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→74.23 Å / Num. obs: 14000 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 60.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Χ2: 1.02 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 2 / Num. unique obs: 1195 / CC1/2: 0.695 / Rpim(I) all: 0.573 / Rrim(I) all: 1.472 / Χ2: 1.02 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5vpt Resolution: 2.2→31.72 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.51 Å2 / Biso mean: 67.4126 Å2 / Biso min: 32.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→31.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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