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- PDB-3u9q: Ligand binding domain of PPARgamma complexed with Decanoic Acid a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3u9q | ||||||
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Title | Ligand binding domain of PPARgamma complexed with Decanoic Acid and PGC-1a peptide | ||||||
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Function / homology | ![]() positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / : / : / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malapaka, V.R. / Xu, H.E. | ||||||
![]() | ![]() Title: Identification and Mechanism of 10-Carbon Fatty Acid as Modulating Ligand of Peroxisome Proliferator-activated Receptors. Authors: Malapaka, R.R. / Khoo, S. / Zhang, J. / Choi, J.H. / Zhou, X.E. / Xu, Y. / Gong, Y. / Li, J. / Yong, E.L. / Chalmers, M.J. / Chang, L. / Resau, J.H. / Griffin, P.R. / Chen, Y.E. / Xu, H.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.4 KB | Display | ![]() |
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PDB format | ![]() | 93 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 30704.734 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain, UNP residues 236-504 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1000.319 Da / Num. of mol.: 1 / Fragment: Peptide, UNP residues 142-150 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-DKA / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion / pH: 6.2 Details: 0.2 M sodium acetate (pH 6.2), 20% PEG 3350, 15% glycerol and 1 mM concentration of the ligand., VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2009 | |||||||||
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.52→33.082 Å / Num. all: 45773 / Num. obs: 43465 / % possible obs: 94.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 | |||||||||
Reflection shell | Resolution: 1.522→1.562 Å / % possible all: 97.64 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100 Å2 / Biso mean: 20.037 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.522→30.082 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.522→1.562 Å / Total num. of bins used: 20
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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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