+Open data
-Basic information
Entry | Database: PDB / ID: 4avq | ||||||
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Title | Influenza strain pH1N1 2009 polymerase subunit PA endonuclease | ||||||
Components | POLYMERASE PA | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / 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: 2.1 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 | 4avq.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4avq.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 4avq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4avq ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avq | HTTPS FTP |
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-Related structure data
Related structure data | 4avgC 4avlC 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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Unit cell |
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Components on special symmetry positions |
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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-MN / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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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: 3.01 Å3/Da / Density % sol: 59.2 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.6 M SODIUM FORMATE 0.1 M HEPES PH 7 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 65996 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.59 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.63 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W69 Resolution: 2.1→49.13 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.157 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.042 / 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: 30.875 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→49.13 Å
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