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- PDB-3bkz: X-ray structure of E coli AlkB crosslinked to dsDNA in the active site -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bkz | ||||||
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Title | X-ray structure of E coli AlkB crosslinked to dsDNA in the active site | ||||||
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![]() | DNA REPAIR / OXIDOREDUCTASE/DNA / alkylation repair / protein DNA interaction / cross-linking / dioxygenase / OXIDOREDUCTASE-DNA COMPLEX | ||||||
Function / homology | ![]() response to methyl methanesulfonate / DNA oxidative demethylase / : / oxidative RNA demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair ...response to methyl methanesulfonate / DNA oxidative demethylase / : / oxidative RNA demethylation / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yi, C. / Yang, C.-G. / 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 | ![]() | 77.9 KB | Display | ![]() |
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PDB format | ![]() | 59.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.7 KB | Display | ![]() |
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Full document | ![]() | 466.8 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bi3C ![]() 3bieC ![]() 3btxC ![]() 3btyC ![]() 3btzC ![]() 3bu0C ![]() 3bucC ![]() 2qxq 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22286.559 Da / Num. of mol.: 1 / Mutation: D135C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P05050, 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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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4050.739 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3934.599 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 294 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AKG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MN / |
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#5: Chemical | ChemComp-AKG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 5000, 0.1M sodium chloride, 25 mM 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. all: 36607 / Num. obs: 36607 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.59→1.65 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2 / % possible all: 87.3 |
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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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.876 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 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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