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Yorodumi- PDB-6e4c: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e4c | ||||||
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Title | The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-6-(2-methyl-4-(5-oxo-4,5-dihydro-1,2,4-oxadiazol-3-yl)phenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / PA endonuclease / inhibitor / influenza / H1N1 / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 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 | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Morrison, C.N. / Dick, B.L. / Credille, C.V. / Cohen, S.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2019 Title: SAR Exploration of Tight-Binding Inhibitors of Influenza Virus PA Endonuclease. Authors: Credille, C.V. / Morrison, C.N. / Stokes, R.W. / Dick, B.L. / Feng, Y. / Sun, J. / Chen, Y. / Cohen, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e4c.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e4c.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e4c_validation.pdf.gz | 690.9 KB | Display | wwPDB validaton report |
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Full document | 6e4c_full_validation.pdf.gz | 694.2 KB | Display | |
Data in XML | 6e4c_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 6e4c_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/6e4c ftp://data.pdbj.org/pub/pdb/validation_reports/e4/6e4c | HTTPS FTP |
-Related structure data
Related structure data | 6e3mC 6e3nC 6e3oC 6e3pC 6e6vC 6e6wC 6e6xC 4awmS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22468.666 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-198) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21 (bacteria) References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HRJ / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.81 % |
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Crystal grow | Temperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 30% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2018 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→44.28 Å / Num. obs: 8894 / % possible obs: 99.9 % / Redundancy: 23.3 % / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.01 / Rrim(I) all: 0.035 / Net I/σ(I): 62.6 |
Reflection shell | Resolution: 2.35→2.44 Å / Redundancy: 24.1 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 831 / Rpim(I) all: 0.13 / Rrim(I) all: 0.475 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4AWM Resolution: 2.35→44.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.356 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.272 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.646 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→44.28 Å
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