+Open data
-Basic information
Entry | Database: PDB / ID: 6ie3 | ||||||
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Title | Crystal structure of methyladenine demethylase | ||||||
Components | Nucleic acid dioxygenase ALKBH1 | ||||||
Keywords | OXIDOREDUCTASE / demethylase / DNA binding protein | ||||||
Function / homology | Function and homology information regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / tRNA wobble cytosine modification / 5-methylcytosine dioxygenase activity / tRNA demethylase activity / regulation of translational elongation / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase / : ...regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / tRNA wobble cytosine modification / 5-methylcytosine dioxygenase activity / tRNA demethylase activity / regulation of translational elongation / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / 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 / DNA alkylation repair / 2-oxoglutarate-dependent dioxygenase activity / oxidative demethylation / DNA demethylation / regulation of translational initiation / chemoattractant activity / developmental growth / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / placenta development / ferrous iron binding / neuron migration / euchromatin / neuron projection development / negative regulation of neuron apoptotic process / in utero embryonic development / tRNA binding / DNA repair / endoplasmic reticulum / mitochondrion / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å | ||||||
Authors | Tian, L.F. / Tang, Q. / Chen, Z.Z. / Yan, X.X. | ||||||
Citation | Journal: Cell Res. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ie3.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ie3.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ie3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/6ie3 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/6ie3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43887.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH1, ABH, ABH1, ALKBH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q13686, DNA N6-methyladenine demethylase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-EOH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 5% ethanol, 5% MPD, 100 mM NaF, 100 mM HepespH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 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: 1.97→50 Å / Num. obs: 24558 / % possible obs: 99.4 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.026 / Rrim(I) all: 0.099 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.97→2 Å / Rmerge(I) obs: 0.746 / Num. unique obs: 621 / Rpim(I) all: 0.232 / Rrim(I) all: 0.783 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.97→49.13 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.163 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.18 / 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: 31.318 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→49.13 Å
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Refine LS restraints |
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