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- PDB-3btx: X-ray structure of human ABH2 bound to dsDNA through active site ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3btx | ||||||
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Title | X-ray structure of human ABH2 bound to dsDNA through active site cross-linking | ||||||
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![]() | Oxidoreductase/DNA / protein/DNA interaction / human dioxygenase / DNA repair / cross-linking / DNA damage / Iron / Metal-binding / Nucleus / Oxidoreductase / Oxidoreductase-DNA COMPLEX | ||||||
Function / homology | ![]() cytosine C-5 DNA demethylase activity / ALKBH2 mediated reversal of alkylation damage / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / rDNA binding / DNA alkylation repair / ferrous iron binding / nucleolus / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yang, C.-G. / Yi, C. / He, C. | ||||||
![]() | ![]() Title: Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Authors: Yang, C.G. / Yi, C. / Duguid, E.M. / Sullivan, C.T. / Jian, X. / Rice, P.A. / He, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.8 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 438.1 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bi3C ![]() 3bieC ![]() 3bkzC ![]() 3btyC ![]() 3btzC ![]() 3bu0C ![]() 3bucC 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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Unit cell |
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Components
#1: Protein | Mass: 23135.430 Da / Num. of mol.: 1 / Mutation: C67S, C165S, C192S, E175C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q6NS38, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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#2: DNA chain | Mass: 4017.701 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 3943.613 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.19 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8% PEG 8000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9266 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 28880 / Num. obs: 28880 / % possible obs: 98.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 44.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2606 / % possible all: 91.9 |
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Processing
Software |
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Refinement | Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.452 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.143 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.73 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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