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Yorodumi- PDB-1xqo: Crystal structure of native Pa-AGOG, 8-oxoguanine DNA glycosylase... -
+Open data
-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 | ||||||
Components | 8-oxoguanine DNA glycosylase | ||||||
Keywords | LYASE / Helix-hairpin-Helix / 8-oxoguanine DNA glycosylase / Archaea / P.aerophilum / Pa-AGOG native / DNA repair | ||||||
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 | Pyrobaculum aerophilum (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.03 Å | ||||||
Authors | Lingaraju, G.M. / Sartori, A.A. / Kostrewa, D. / Prota, A.E. / Jiricny, J. / Winkler, F.K. | ||||||
Citation | Journal: Structure / Year: 2005 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: Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xqo.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xqo.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 1xqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xqo_validation.pdf.gz | 264.2 KB | Display | wwPDB validaton report |
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Full document | 1xqo_full_validation.pdf.gz | 264.1 KB | Display | |
Data in XML | 1xqo_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/1xqo ftp://data.pdbj.org/pub/pdb/validation_reports/xq/1xqo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biologically active unit is a monomer. |
-Components
#1: Protein | Mass: 29511.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: Pa-AGOG / Plasmid: pET28C(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8ZVK6 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.03→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.906 / SU ML: 0.02 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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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