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- PDB-7xwr: Human Estrogen Receptor beta Ligand-binding Domain in Complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xwr | ||||||
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Title | Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile | ||||||
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![]() | TRANSCRIPTION/INHIBITOR / Inhibitor / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex | ||||||
Function / homology | ![]() receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Furuya, N. / Handa, C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives. Authors: Handa, C. / Yamazaki, Y. / Yonekubo, S. / Furuya, N. / Momose, T. / Ozawa, T. / Furuishi, T. / Fukuzawa, K. / Yonemochi, 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 | ![]() | 188.1 KB | Display | ![]() |
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PDB format | ![]() | 145.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 952 KB | Display | ![]() |
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Full document | ![]() | 956 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xvyC ![]() 7xvzC ![]() 7xwpC ![]() 7xwqC ![]() 2giuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 27702.578 Da / Num. of mol.: 2 / Fragment: ligand-binding domain / Mutation: C334S,C369S,C481S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→46.633 Å / Num. obs: 25917 / % possible obs: 99.3 % / Redundancy: 5.9 % / CC1/2: 0.937 / Rmerge(I) obs: 0.451 / Rpim(I) all: 0.288 / Rrim(I) all: 0.537 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2.16→2.23 Å / Redundancy: 5.7 % / Rmerge(I) obs: 2.186 / Num. unique obs: 2196 / CC1/2: 0.623 / Rpim(I) all: 1.499 / Rrim(I) all: 2.664 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2giu Resolution: 2.164→46.633 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.338 / WRfactor Rwork: 0.264 / SU B: 12.339 / SU ML: 0.294 / Average fsc free: 0.7829 / Average fsc work: 0.8042 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.269 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.142 Å2
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Refinement step | Cycle: LAST / Resolution: 2.164→46.633 Å
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Refine LS restraints |
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LS refinement shell |
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