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- PDB-4awm: 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: 4awm | ||||||
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Title | Influenza strain pH1N1 2009 polymerase subunit PA endonuclease in complex with (-)-epigallocatechin gallate from green tea | ||||||
![]() | POLYMERASE PA | ||||||
![]() | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / HYDROLASE / MANGANESE-DEPENDENT / PD...D-E...K SUPERFAMILY | ||||||
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. / Ruigrok, R.W. / 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 | ![]() | 55.6 KB | Display | ![]() |
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PDB format | ![]() | 39 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4avgC ![]() 4avlC ![]() 4avqC ![]() 4awfC ![]() 4awgC ![]() 4awhC ![]() 4awkC ![]() 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 on special symmetry positions |
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Components
#1: Protein | Mass: 22468.666 Da / Num. of mol.: 1 / Fragment: ENDONUCLEASE, RESIDUES 1-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.8 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 10% PEG 3350, 0.1 M NACL, 0.1 M HEPES PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 7797 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.14 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W69 Resolution: 2.6→42.78 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU B: 11.63 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.072 / 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: 38.275 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→42.78 Å
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Refine LS restraints |
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