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- PDB-6i67: Crystal structure of human ERRg LBD in complex with tetrahydro-2-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i67 | ||||||
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Title | Crystal structure of human ERRg LBD in complex with tetrahydro-2-naphtol | ||||||
![]() | Estrogen-related receptor gamma | ||||||
![]() | NUCLEAR PROTEIN / transcription factor nuclear receptor endocrine disruptor | ||||||
Function / homology | ![]() AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis ...AF-2 domain binding / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Delfosse, V. / Blanc, P. / Bourguet, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the activation mechanism of human estrogen-related receptor gamma by environmental endocrine disruptors. Authors: Thouennon, E. / Delfosse, V. / Bailly, R. / Blanc, P. / Boulahtouf, A. / Grimaldi, M. / Barducci, A. / Bourguet, W. / Balaguer, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 68.8 KB | Display | ![]() |
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PDB format | ![]() | 48.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.5 KB | Display | ![]() |
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Full document | ![]() | 443.6 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i61C ![]() 6i62C ![]() 6i63C ![]() 6i64C ![]() 6i65C ![]() 6i66C ![]() 2zbsS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27300.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-H42 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0-100 mM Sodium acetate 100 mM Tris 23-26% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→45.315 Å / Num. obs: 53683 / % possible obs: 100 % / Redundancy: 12.2 % / Rrim(I) all: 0.082 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4120 / Rrim(I) all: 0.559 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZBS Resolution: 1.75→45.315 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.64 / Phase error: 21.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→45.315 Å
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Refine LS restraints |
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LS refinement shell |
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