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- PDB-6w7a: The crystal structure of the 2009/H1N1/California PA endonuclease... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w7a | ||||||
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Title | The crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to DNA oligomer TAGCAT (uncleaved, 5mM overnight DNA soak) | ||||||
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![]() | VIRAL PROTEIN/DNA / NUCLEASE / INFLUENZA / DNA oligomer / uncleaved / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuypers, M.G. / Kumar, G. / Webb, T. / White, S.W. | ||||||
![]() | ![]() Title: Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism. Authors: Kumar, G. / Cuypers, M. / Webby, R.R. / Webb, T.R. / White, S.W. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 75.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 875.5 KB | Display | ![]() |
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Full document | ![]() | 875.7 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6whmC ![]() 6ws3C ![]() 7kafC ![]() 7kbcC ![]() 7kl3C ![]() 5vptS ![]() 6w5p S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein / DNA chain , 2 types, 2 molecules AB
#1: Protein | Mass: 23134.316 Da / Num. of mol.: 1 / Mutation: E119D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: PA-X, PA / Variant: H1N1/California/2009 / Strain: A/Luxembourg/43/2009(H1N1) / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 2416.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ssDNA / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 115 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MN / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE / Temp details: controlled temperature room |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 16288 / % possible obs: 98.9 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.08→2.15 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1435 / CC1/2: 0.865 / Rpim(I) all: 0.219 / Rrim(I) all: 0.594 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5vpt Resolution: 2.09→39.95 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.9 Details: refmac5 then rigid body with phenix.refine for final check
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.35 Å2 / Biso mean: 57.9536 Å2 / Biso min: 28.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→39.95 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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