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Open data
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Basic information
Entry | Database: PDB / ID: 6ie2 | ||||||
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Title | Crystal structure of methyladenine demethylase | ||||||
![]() | Nucleic acid dioxygenase ALKBH1 | ||||||
![]() | OXIDOREDUCTASE / demethylase / DNA BINDING PROTEIN | ||||||
Function / homology | ![]() regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / regulation of translational elongation / 5-methylcytosine dioxygenase activity / tRNA demethylase activity / regulation of mitochondrial translation / tRNA wobble cytosine modification / DNA oxidative demethylase / : / oxidative RNA demethylation ...regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / regulation of translational elongation / 5-methylcytosine dioxygenase activity / tRNA demethylase activity / regulation of mitochondrial translation / tRNA wobble cytosine modification / DNA oxidative demethylase / : / oxidative RNA demethylation / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / 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 / RNA repair / : / oxidative demethylation / 2-oxoglutarate-dependent dioxygenase activity / DNA alkylation repair / regulation of translational initiation / chemoattractant activity / developmental growth / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / neuron migration / euchromatin / placenta development / ferrous iron binding / neuron projection development / in utero embryonic development / negative regulation of neuron apoptotic process / tRNA binding / DNA repair / endoplasmic reticulum / mitochondrion / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tian, L.F. / Tang, Q. / Chen, Z.Z. / Yan, X.X. | ||||||
![]() | ![]() Title: Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1. Authors: Tian, L.F. / Liu, Y.P. / Chen, L. / Tang, Q. / Wu, W. / Sun, W. / Chen, Z. / Yan, X.X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 517.5 KB | Display | ![]() |
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PDB format | ![]() | 422.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 522 KB | Display | ![]() |
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Full document | ![]() | 562.6 KB | Display | |
Data in XML | ![]() | 96.1 KB | Display | |
Data in CIF | ![]() | 128.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ie3SC 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
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Components
#1: Protein | Mass: 43887.684 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13686, DNA N6-methyladenine demethylase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-AKG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.65 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5% PEG3350, 5% MPD, 100mM CaCl2, 200mM NaF, 100mM Bis-Tris pH6.5 PH range: 6.2-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50.01 Å / Num. obs: 72797 / % possible obs: 93 % / Redundancy: 3.7 % / CC1/2: 0.978 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.056 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.8→2.85 Å / Rmerge(I) obs: 0.72 / Num. unique obs: 1351 / CC1/2: 0.643 / Rpim(I) all: 0.556 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6IE3 Resolution: 2.8→50.01 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.611 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.212 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→50.01 Å
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Refine LS restraints |
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