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- PDB-2yg9: Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yg9 | ||||||
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Title | Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans | ||||||
![]() | DNA-3-methyladenine glycosidase II, putative | ||||||
![]() | HYDROLASE / DNA REPAIR | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moe, E. / Hall, D.R. / Leiros, I. / Talstad, V. / Timmins, J. / McSweeney, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.5 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2yg8SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: (0.94456, -0.0149, 0.32801), Vector: |
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Components
#1: Protein | Mass: 23828.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DR_2584 / Production host: ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.6 % / 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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRROR |
Radiation | Monochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→42.68 Å / Num. obs: 35790 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 12.76 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YG8 Resolution: 1.95→42.68 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.454 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.152 / 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: 9.348 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→42.68 Å
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Refine LS restraints |
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