+Open data
-Basic information
Entry | Database: PDB / ID: 5dab | ||||||
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Title | Crystal structure of FTO-IN115 | ||||||
Components | Alpha-ketoglutarate-dependent dioxygenase FTO | ||||||
Keywords | OXIDOREDUCTASE / Fat mass and obesity associated (FTO) protein / small molecule | ||||||
Function / homology | Function and homology information regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / : ...regulation of white fat cell proliferation / tRNA demethylase activity / Reversal of alkylation damage by DNA dioxygenases / mRNA N6-methyladenine demethylase / mRNA N6-methyladenosine dioxygenase activity / regulation of respiratory system process / regulation of lipid storage / : / regulation of brown fat cell differentiation / : / : / 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 / oxidative demethylation / DNA demethylation / temperature homeostasis / mRNA destabilization / regulation of multicellular organism growth / adipose tissue development / ferrous iron binding / transferase activity / nuclear speck / intracellular membrane-bounded organelle / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Chai, J. / Zhou, B. / Liu, W. / Han, Z. / Niu, T. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of FTO-IN115 Authors: Chai, J. / Zhou, B. / Liu, W. / Han, Z. / Niu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dab.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dab.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5dab ftp://data.pdbj.org/pub/pdb/validation_reports/da/5dab | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55090.184 Da / Num. of mol.: 1 / Fragment: UNP residues 33-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTO, KIAA1752 / Production host: Escherichia coli (E. coli) References: UniProt: Q9C0B1, 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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-Non-polymers , 5 types, 130 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-FE2 / | #4: Chemical | ChemComp-AKG / | #5: Chemical | ChemComp-58W / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 61.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10%(w/v) polyethylene glycol (PEG) 3350, 0.1 M trisodium citrate dehydrate, 3.0 mM N-oxalylglycine (NOG) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 35070 / % possible obs: 96.7 % / Redundancy: 3.7 % / Net I/σ(I): 30.1 |
-Processing
Software |
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Refinement | Resolution: 2.1→28.908 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.16 Å2 / ksol: 0.392 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.908 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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