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Yorodumi- PDB-7p0w: Crystal structure of a trapped Pab-AGOG/double-standed DNA covale... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p0w | ||||||
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Title | Crystal structure of a trapped Pab-AGOG/double-standed DNA covalent intermediate (DNA containing thymine opposite to lesion) | ||||||
Components |
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Keywords | HYDROLASE / 8-oxoguanine DNA glycosylase / AGOG / Pyrococcus abyssi / trapped double-stranded DNA intermediate | ||||||
Function / homology | Function and homology information oxidized base lesion DNA N-glycosylase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.12 Å | ||||||
Authors | Coste, F. / Goffinont, S. / Flament, D. / Castaing, B. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing. Authors: Franck, C. / Stephane, G. / Julien, C. / Virginie, G. / Martine, G. / Norbert, G. / Fabrice, C. / Didier, F. / Josef, S.M. / Bertrand, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p0w.cif.gz | 203.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p0w.ent.gz | 160.4 KB | Display | PDB format |
PDBx/mmJSON format | 7p0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p0w_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 7p0w_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 7p0w_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 7p0w_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/7p0w ftp://data.pdbj.org/pub/pdb/validation_reports/p0/7p0w | HTTPS FTP |
-Related structure data
Related structure data | 7olbC 7oliC 7ou3C 7oueC 7oy7SC 7p8lC 7p9zC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27982.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Strain: GE5 / Orsay / Gene: PYRAB10170, PAB1695 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UZY0, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase |
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-DNA chain , 2 types, 2 molecules BI
#2: DNA chain | Mass: 2555.686 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TTT(PED)TTTCT / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 2780.889 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 413 molecules
#4: Chemical | #5: Chemical | #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: 2.23 Å3/Da / Density % sol: 44.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: MgCl2, Na acetate pH5.0, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→45.88 Å / Num. obs: 114280 / % possible obs: 99.4 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.12→1.14 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5266 / CC1/2: 0.834 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OY7 Resolution: 1.12→34.65 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.86 Å2 / Biso mean: 18.223 Å2 / Biso min: 7.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.12→34.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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