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Yorodumi- PDB-2yg8: Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yg8 | ||||||
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Title | Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans | ||||||
Components | DNA-3-methyladenine glycosidase II, putative | ||||||
Keywords | HYDROLASE / DNA REPAIR | ||||||
Function / homology | Function and homology information alkylated DNA binding / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / base-excision repair, AP site formation / DNA alkylation repair / protein-DNA complex / cytoplasm Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Moe, E. / Hall, D.R. / Leiros, I. / Talstad, V. / Timmins, J. / McSweeney, S. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012 Title: Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans. Authors: Moe, E. / Hall, D.R. / Leiros, I. / Monsen, V.T. / Timmins, J. / McSweeney, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yg8.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yg8.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/2yg8 ftp://data.pdbj.org/pub/pdb/validation_reports/yg/2yg8 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.94436, -0.01429, 0.3286), Vector: |
-Components
#1: Protein | Mass: 23969.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: DR_2584 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: Q9RRB0 #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.8 % / Description: NONE |
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Crystal grow | Details: 1 UL DROPS OF 10 MG/ML PROTEIN MIXED WITH A SOLUTION CONTAINING 1 M LICL2, 0.1 M MES PH 6.0 AND 10% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97949 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR |
Radiation | Monochromator: CHANNEL CUT SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.75 Å / Num. obs: 33423 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2→49.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.03 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 8.644 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.75 Å
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