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Yorodumi- PDB-4w9s: 2-(4-(1H-tetrazol-5-yl)phenyl)-5-hydroxypyrimidin-4(3H)-one bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4w9s | ||||||
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Title | 2-(4-(1H-tetrazol-5-yl)phenyl)-5-hydroxypyrimidin-4(3H)-one bound to influenza 2009 H1N1 endonuclease | ||||||
Components | Polymerase acidic protein | ||||||
Keywords | transcription/transcription inhibitor / CAP-SNATCHING / RNA BINDING PROTEIN / RNA BINDING PROTEIN-INHIBITOR COMPLEX / transcription-transcription inhibitor complex | ||||||
Function / homology | Function and homology information 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 | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bauman, J.D. / Patel, D. / Das, K. / Arnold, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Phenyl Substituted 4-Hydroxypyridazin-3(2H)-ones and 5-Hydroxypyrimidin-4(3H)-ones: Inhibitors of Influenza A Endonuclease. Authors: Sagong, H.Y. / Bauman, J.D. / Patel, D. / Das, K. / Arnold, E. / LaVoie, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w9s.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w9s.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 4w9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w9s_validation.pdf.gz | 753.7 KB | Display | wwPDB validaton report |
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Full document | 4w9s_full_validation.pdf.gz | 755.4 KB | Display | |
Data in XML | 4w9s_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4w9s_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/4w9s ftp://data.pdbj.org/pub/pdb/validation_reports/w9/4w9s | HTTPS FTP |
-Related structure data
Related structure data | 4m5qS 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: 28505.270 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Duck/Hokkaido/8/1980 H3N8 / Gene: PA / Plasmid: PCDF-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P13166 | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-3K1 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: Crystals are formed by mixing in a 1:1 ratio endonuclease (5 mg/ml) with crystallization buffer containing 200 mM MES, 27% PEG8000, 200 mM ammonium sulfate, 1 mM manganese chloride, 10 mM ...Details: Crystals are formed by mixing in a 1:1 ratio endonuclease (5 mg/ml) with crystallization buffer containing 200 mM MES, 27% PEG8000, 200 mM ammonium sulfate, 1 mM manganese chloride, 10 mM magnesium acetate, 10 mM taurine, and 50 mM sodium fluoride. Crystals form within a few hours and grow to maximum size in one to two weeks |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: . X-ray diffraction data collection was performed at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline. The diffraction data were indexed, processed, scaled and ...Ambient temp details: . X-ray diffraction data collection was performed at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline. The diffraction data were indexed, processed, scaled and merged using HKL2000.29 The structure was solved and refined using the software PHENIX.30 |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.9 Å / Num. all: 27807 / Num. obs: 27807 / % possible obs: 99.31 % / Redundancy: 3.5 % / Net I/σ(I): 22.39 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 1.83 / % possible all: 99.2 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M5Q Resolution: 1.8→22.9 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.8→22.9 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 |
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