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Yorodumi- PDB-4avg: Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in... -
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-Basic information
Entry | Database: PDB / ID: 4avg | ||||||
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Title | Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with diketo compound 2 | ||||||
Components | POLYMERASE PA | ||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE / MANGANESE-DEPENDENT | ||||||
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: 2.2 Å | ||||||
Authors | Kowalinski, E. / Zubieta, C. / Wolkerstorfer, A. / Szolar, O.H. / Ruigrok, R.W. / Cusack, S. | ||||||
Citation | Journal: Plos Pathog. / Year: 2012 Title: Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza Ph1N1 (2009) Polymerase. Authors: Kowalinski, E. / Zubieta, C. / Wolkerstorfer, A. / Szolar, O.H. / Ruigrok, R.W. / Cusack, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4avg.cif.gz | 176.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4avg.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 4avg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4avg_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4avg_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4avg_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 4avg_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4avg ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avg | HTTPS FTP |
-Related structure data
Related structure data | 4avlC 4avqC 4awfC 4awgC 4awhC 4awkC 4awmC 2w69S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 23939.291 Da / Num. of mol.: 4 / Fragment: ENDONUCLEASE, RESIDUES 1-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/CALIFORNIA/04/2009 (H1N1) / Description: SYNTHETIC GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3W5S0 #2: Chemical | ChemComp-SL6 / ( #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | Sequence details | GENBANK NUMBER ACP44156 | |
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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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 25% PEG 3350, 0.1 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 45289 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.51 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.44 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W69 Resolution: 2.2→43.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.434 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.692 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→43.96 Å
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Refine LS restraints |
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