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- PDB-4avl: Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4avl | ||||||
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Title | Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with dTMP | ||||||
![]() | POLYMERASE PA | ||||||
![]() | HYDROLASE / ENDONUCLEASE / MANGANESE-DEPENDENT | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kowalinski, E. / Zubieta, C. / Wolkerstorfer, A. / Szolar, O.H.J. / Ruigrok, R.W.H. / Cusack, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340 KB | Display | ![]() |
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PDB format | ![]() | 278.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 32.9 KB | Display | |
Data in CIF | ![]() | 44.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4avgC ![]() 4avqC ![]() 4awfC ![]() 4awgC ![]() 4awhC ![]() 4awkC ![]() 4awmC ![]() 2w69S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-TMP / #4: Water | ChemComp-HOH / | Sequence details | GENBANK NUMBER ACP44156 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 25% PEG 3350 0.1 M BIS-TRIS PH 5.5 0.2 M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→50 Å / Num. obs: 71829 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.02 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.87→1.92 Å / Redundancy: 5.17 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.22 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W69 Resolution: 1.87→41.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.232 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→41.8 Å
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Refine LS restraints |
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