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Yorodumi- PDB-6imc: Crystal Structure of ALKBH1 in complex with Mn(II) and N-Oxalylglycine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6imc | ||||||
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Title | Crystal Structure of ALKBH1 in complex with Mn(II) and N-Oxalylglycine | ||||||
Components | Nucleic acid dioxygenase ALKBH1 | ||||||
Keywords | GENE REGULATION / double-stranded beta helix | ||||||
Function / homology | Function and homology information positive regulation of gene expression, epigenetic / regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA wobble cytosine modification / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase ...positive regulation of gene expression, epigenetic / regulation of translational initiation by tRNA modification / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / regulation of translational elongation / tRNA wobble cytosine modification / tRNA demethylase activity / oxidative RNA demethylation / regulation of mitochondrial translation / DNA oxidative demethylase / 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 / 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 / placenta development / neuron migration / ferrous iron binding / euchromatin / neuron projection development / regulation of gene expression / in utero embryonic development / negative regulation of neuron apoptotic process / cell differentiation / tRNA binding / endoplasmic reticulum / mitochondrion / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å | ||||||
Authors | Zhang, M. / Yang, S. / Zhao, W. / Li, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Res. / Year: 2020 Title: Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA. Authors: Zhang, M. / Yang, S. / Nelakanti, R. / Zhao, W. / Liu, G. / Li, Z. / Liu, X. / Wu, T. / Xiao, A. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6imc.cif.gz | 287.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6imc.ent.gz | 230.1 KB | Display | PDB format |
PDBx/mmJSON format | 6imc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6imc_validation.pdf.gz | 480.5 KB | Display | wwPDB validaton report |
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Full document | 6imc_full_validation.pdf.gz | 491.6 KB | Display | |
Data in XML | 6imc_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 6imc_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/6imc ftp://data.pdbj.org/pub/pdb/validation_reports/im/6imc | HTTPS FTP |
-Related structure data
Related structure data | 6imaSC 6ksfC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 40587.375 Da / Num. of mol.: 4 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Alkbh1, Abh, Alkbh / Plasmid: pRSFDuet-P3C / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0CB42, 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 ...References: UniProt: P0CB42, 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 N6-methyladenine demethylase, DNA-(apurinic or apyrimidinic site) lyase, DNA oxidative demethylase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-OGA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 63.33 % / Mosaicity: 0.311 ° / Mosaicity esd: 0.003 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 10% PEG6000, 0.1 M Bicine-HCL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2017 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 64730 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Χ2: 0.532 / Net I/σ(I): 5.3 / Num. measured all: 388280 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.683
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IMA Resolution: 2.51→35.164 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 25.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.77 Å2 / Biso mean: 46.2396 Å2 / Biso min: 18.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.51→35.164 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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