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Yorodumi- PDB-4nrq: Crystal structure of human ALKBH5 in complex with pyridine-2,4-di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nrq | ||||||
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Title | Crystal structure of human ALKBH5 in complex with pyridine-2,4-dicarboxylate | ||||||
Components | RNA demethylase ALKBH5 | ||||||
Keywords | OXIDOREDUCTASE / alkbh5 / 6-methyl adenosine / PROTEIN/DNA INTERACTION / HUMAN DIOXYGENASE / METAL-BINDING / NUCLEUS / demethylation / RNA REPAIR | ||||||
Function / homology | Function and homology information gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of mRNA export from nucleus / oxidative RNA demethylase activity / regulation of mRNA processing / paraspeckles / non-membrane-bounded organelle assembly / 2-oxoglutarate-dependent dioxygenase activity ...gamma-delta T cell proliferation / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of mRNA export from nucleus / oxidative RNA demethylase activity / regulation of mRNA processing / paraspeckles / non-membrane-bounded organelle assembly / 2-oxoglutarate-dependent dioxygenase activity / mRNA destabilization / mRNA export from nucleus / molecular condensate scaffold activity / mRNA processing / regulation of translation / spermatogenesis / cell differentiation / response to hypoxia / nuclear speck / Golgi apparatus / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Feng, C. / Chen, Z. / Liu, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition Authors: Feng, C. / Liu, Y. / Wang, G. / Deng, Z. / Zhang, Q. / Wu, W. / Tong, Y. / Cheng, C. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nrq.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nrq.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 4nrq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nrq_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 4nrq_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 4nrq_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4nrq_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/4nrq ftp://data.pdbj.org/pub/pdb/validation_reports/nr/4nrq | HTTPS FTP |
-Related structure data
Related structure data | 4nrmSC 4nroC 4nrpC 4o7xC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26385.127 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 66-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ABH5, ALKBH5, OFOXD1 / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) References: UniProt: Q6P6C2, 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 |
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#2: Chemical | ChemComp-PD2 / |
#3: Chemical | ChemComp-MN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.32 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG 4K, 100mM CH3CO2NH4, 100mM Na-citrate , pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jun 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 8780 / Num. obs: 8721 / % possible obs: 99 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 2.5→2.54 Å / % possible all: 98 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NRM Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.909 / SU B: 19.573 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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