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Yorodumi- PDB-6w7a: The crystal structure of the 2009/H1N1/California PA endonuclease... -
+Open data
-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) | ||||||
Components |
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Keywords | VIRAL PROTEIN/DNA / NUCLEASE / INFLUENZA / DNA oligomer / uncleaved / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Influenza A virus synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Cuypers, M.G. / Kumar, G. / Webb, T. / White, S.W. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w7a.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w7a.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 6w7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w7a_validation.pdf.gz | 875.5 KB | Display | wwPDB validaton report |
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Full document | 6w7a_full_validation.pdf.gz | 875.7 KB | Display | |
Data in XML | 6w7a_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 6w7a_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w7a ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w7a | HTTPS FTP |
-Related structure data
Related structure data | 6whmC 6ws3C 7kafC 7kbcC 7kl3C 5vptS 6w5p S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Influenza A virus, (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1)) Gene: PA-X, PA / Variant: H1N1/California/2009 / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P2TE19, UniProt: C6H0Y9 |
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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
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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