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- PDB-8jnk: Crystal structure of human ALKBH3 bound to ssDNA through active s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8jnk | ||||||
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Title | Crystal structure of human ALKBH3 bound to ssDNA through active site crosslink | ||||||
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![]() | RNA BINDING PROTEIN / RNA m1A demethylase | ||||||
Function / homology | ![]() mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding ...mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding / ferrous iron binding / cell population proliferation / DNA repair / mitochondrion / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation. Authors: Zhang, L. / Duan, H.C. / Paduch, M. / Hu, J. / Zhang, C. / Mu, Y. / Lin, H. / He, C. / Kossiakoff, A.A. / Jia, G. / Zhang, L. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 510.8 KB | Display | ![]() |
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PDB format | ![]() | 412.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 572.2 KB | Display | ![]() |
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Full document | ![]() | 613.6 KB | Display | |
Data in XML | ![]() | 90 KB | Display | |
Data in CIF | ![]() | 121 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jnrC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 8 molecules IJKLMNOP
#3: Antibody | Mass: 22927.537 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Antibody | Mass: 23667.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein / DNA chain , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 27013.326 Da / Num. of mol.: 4 / Mutation: C110S, D189S, C201S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q96Q83, DNA oxidative demethylase, mRNA N1-methyladenine demethylase #2: DNA chain | Mass: 1844.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 285 molecules ![](data/chem/img/OGA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-OGA / #6: Chemical | ChemComp-MN / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaCl, 20%PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.69→50 Å / Num. obs: 92893 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Χ2: 1.265 / Net I/σ(I): 11 / Num. measured all: 348882 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→46.9 Å
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Refine LS restraints |
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LS refinement shell |
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