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- PDB-6dcz: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dcz | ||||||
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Title | The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-4-oxo-4H-pyran-2-carboxylic acid | ||||||
![]() | Polymerase acidic protein | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Endonuclease / Influenza / PA domain / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 | ![]() ![]() | ||||||
![]() | Dick, B.L. / Morrison, C.N. / Cohen, S.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. Authors: Credille, C.V. / Dick, B.L. / Morrison, C.N. / Stokes, R.W. / Adamek, R.N. / Wu, N.C. / Wilson, I.A. / Cohen, S.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.5 KB | Display | ![]() |
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PDB format | ![]() | 36.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 726.9 KB | Display | ![]() |
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Full document | ![]() | 728.5 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dcyC ![]() 6dzqC ![]() 6e0qC ![]() 4awmS S: Starting model for refinement C: citing same article ( |
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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: 22468.666 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-198) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds | ||
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#2: Chemical | ChemComp-G5Y / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 308 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG4000, 100 mM Tris, pH 8.0, 200 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: Oct 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→30.33 Å / Num. obs: 4826 / % possible obs: 95.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.89→3.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 773 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4AWM Resolution: 2.89→28.89 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.85 / SU B: 17.7 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.495 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.918 Å2
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Refinement step | Cycle: 1 / Resolution: 2.89→28.89 Å
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Refine LS restraints |
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