+Open data
-Basic information
Entry | Database: PDB / ID: 6ie2 | ||||||
---|---|---|---|---|---|---|---|
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ie2.cif.gz | 517.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ie2.ent.gz | 422.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ie2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/6ie2 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/6ie2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ie3SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 43887.684 Da / Num. of mol.: 8 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 #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-AKG / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.65 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→50.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|