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Yorodumi- PDB-7olb: Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7olb | ||||||
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Title | Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi | ||||||
Components | N-glycosylase/DNA lyase | ||||||
Keywords | HYDROLASE / 8-oxoguanine DNA glycosylase / Archaea / Pyrococcus abyssi | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 | 7olb.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7olb.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 7olb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7olb_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 7olb_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 7olb_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 7olb_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/7olb ftp://data.pdbj.org/pub/pdb/validation_reports/ol/7olb | HTTPS FTP |
-Related structure data
Related structure data | 7oliC 7ou3C 7oueC 7oy7C 7p0wC 7p8lC 7p9zC 1xg7S 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 , 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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-Non-polymers , 5 types, 207 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CIT / | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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 Å3/Da / Density % sol: 38.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: LiCl, tri-Na citrate, PEG6000 |
-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: Sep 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→46.17 Å / Num. obs: 84275 / % possible obs: 95.7 % / Redundancy: 7 % / Biso Wilson estimate: 11.38 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.1→1.12 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 4021 / CC1/2: 0.954 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1xg7 Resolution: 1.1→46.17 Å / SU ML: 0.0902 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 15.0718 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 17.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→46.17 Å
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Refine LS restraints |
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LS refinement shell |
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