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- PDB-1xqo: Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xqo | ||||||
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Title | Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum | ||||||
![]() | 8-oxoguanine DNA glycosylase | ||||||
![]() | LYASE / Helix-hairpin-Helix / 8-oxoguanine DNA glycosylase / Archaea / P.aerophilum / Pa-AGOG native / DNA repair | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lingaraju, G.M. / Sartori, A.A. / Kostrewa, D. / Prota, A.E. / Jiricny, J. / Winkler, F.K. | ||||||
![]() | ![]() Title: A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure Authors: Lingaraju, G.M. / Sartori, A.A. / Kostrewa, D. / Prota, A.E. / Jiricny, J. / Winkler, F.K. #1: ![]() Title: A novel highly thermostable 8-oxoguanine DNA glycosylase from Pyrobaculum aerophilum Authors: Sartori, A.A. / Lingaraju, G.M. / Hunziker, P. / Winkler, F.K. / Jiricny, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.4 KB | Display | ![]() |
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PDB format | ![]() | 101.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.5 KB | Display | ![]() |
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Full document | ![]() | 397.4 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 11.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biologically active unit is a monomer. |
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Components
#1: Protein | Mass: 29511.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000, HEPES-NaOH, NaCl, Dithio threitol., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 30, 2003 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→57.74 Å / Num. all: 587271 / Num. obs: 116782 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.058 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.03→1.1 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 17208 / Rsym value: 0.468 / % possible all: 78.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.567 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.03→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.03→1.057 Å / Total num. of bins used: 20 /
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