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Yorodumi- PDB-6i65: Crystal structure of human ERRg LBD in complex with 4-iso-propylphenol -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i65 | ||||||
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Title | Crystal structure of human ERRg LBD in complex with 4-iso-propylphenol | ||||||
Components | Estrogen-related receptor gamma | ||||||
Keywords | NUCLEAR PROTEIN / transcription factor nuclear receptor endocrine disruptor | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Delfosse, V. / Blanc, P. / Bourguet, W. | ||||||
Funding support | France, 1items
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Citation | Journal: Cell.Mol.Life Sci. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i65.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i65.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 6i65.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i65_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
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Full document | 6i65_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 6i65_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6i65_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/6i65 ftp://data.pdbj.org/pub/pdb/validation_reports/i6/6i65 | HTTPS FTP |
-Related structure data
Related structure data | 6i61C 6i62C 6i63C 6i64C 6i66C 6i67C 2zbsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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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.) Homo sapiens (human) / Gene: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3 / Plasmid: pDB-His-GST / Production host: Escherichia coli (E. coli) / References: UniProt: P62508 |
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#2: Chemical | ChemComp-H3Z / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 0-100 mM Sodium acetat 100 mM Tris 23-26% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 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: 1.5→46.98 Å / Num. obs: 47226 / % possible obs: 100 % / Redundancy: 12.2 % / Rrim(I) all: 0.054 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 6758 / Rrim(I) all: 0.559 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZBS Resolution: 1.5→46.978 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 19.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→46.978 Å
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Refine LS restraints |
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LS refinement shell |
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