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- PDB-7axi: Crystal structure of the hPXR-LBD in complex with estradiol and c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7axi | ||||||||||||
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Title | Crystal structure of the hPXR-LBD in complex with estradiol and cis-chlordane | ||||||||||||
![]() | Nuclear receptor subfamily 1 group I member 2 | ||||||||||||
![]() | NUCLEAR PROTEIN / NUCLEAR RECEPTOR HORMONE RECEPTOR PREGNANE X RECEPTOR | ||||||||||||
Function / homology | ![]() xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Huet, T. / Delfosse, V. / Bourguet, W. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanistic insights into the synergistic activation of the RXR-PXR heterodimer by endocrine disruptor mixtures. Authors: Delfosse, V. / Huet, T. / Harrus, D. / Granell, M. / Bourguet, M. / Gardia-Parege, C. / Chiavarina, B. / Grimaldi, M. / Le Mevel, S. / Blanc, P. / Huang, D. / Gruszczyk, J. / Demeneix, B. / ...Authors: Delfosse, V. / Huet, T. / Harrus, D. / Granell, M. / Bourguet, M. / Gardia-Parege, C. / Chiavarina, B. / Grimaldi, M. / Le Mevel, S. / Blanc, P. / Huang, D. / Gruszczyk, J. / Demeneix, B. / Cianferani, S. / Fini, J.B. / Balaguer, P. / Bourguet, W. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.7 KB | Display | ![]() |
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PDB format | ![]() | 54.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ax8C ![]() 7ax9C ![]() 7axaC ![]() 7axbC ![]() 7axcC ![]() 7axdC ![]() 7axeC ![]() 7axfC ![]() 7axgC ![]() 7axhC ![]() 7axjC ![]() 7axkC ![]() 7axlC ![]() 1ilgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36280.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 124 molecules ![](data/chem/img/EST.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/S6E.gif)
![](data/chem/img/S6H.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/S6E.gif)
![](data/chem/img/S6H.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EST / |
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#3: Chemical | ChemComp-MPD / ( |
#4: Chemical | ChemComp-S6E / (-) |
#5: Chemical | ChemComp-S6H / (+) |
#6: Chemical | ChemComp-IPA / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 50 - 100 mM imidazole 8 - 14% isopropanol / PH range: 7.0 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→45.952 Å / Num. obs: 20581 / % possible obs: 100 % / Redundancy: 6.8 % / Rrim(I) all: 0.082 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.15→2.27 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2927 / Rrim(I) all: 0.472 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ILG Resolution: 2.15→45.952 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 20 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.23 Å2 / Biso mean: 35.7588 Å2 / Biso min: 14.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→45.952 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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