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Yorodumi- PDB-1s9p: crystal structure of the ligand-binding domain of the estrogen-re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s9p | ||||||
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Title | crystal structure of the ligand-binding domain of the estrogen-related receptor gamma in complex with diethylstilbestrol | ||||||
Components | Estrogen-related receptor gamma | ||||||
Keywords | TRANSCRIPTION / ligand-binding domain / antagonist complex | ||||||
Function / homology | Function and homology information Nuclear Receptor transcription pathway / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear receptor activity / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific ...Nuclear Receptor transcription pathway / nuclear steroid receptor activity / retinoic acid receptor signaling pathway / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / steroid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear receptor activity / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / calmodulin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å | ||||||
Authors | Greschik, H. / Flaig, R. / Renaud, J.P. / Moras, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural Basis for the Deactivation of the Estrogen-related Receptor {gamma} by Diethylstilbestrol or 4-Hydroxytamoxifen and Determinants of Selectivity. Authors: Greschik, H. / Flaig, R. / Renaud, J.P. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s9p.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s9p.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 1s9p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s9p_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1s9p_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 1s9p_validation.xml.gz | 35.5 KB | Display | |
Data in CIF | 1s9p_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/1s9p ftp://data.pdbj.org/pub/pdb/validation_reports/s9/1s9p | HTTPS FTP |
-Related structure data
Related structure data | 1s9qC 1tfcC 1vjbC 1kv6S S: Starting model for refinement C: citing same article (ref.) |
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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: 25787.002 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: ESRRG, NR3B3, ERRG2, ERR3, KIAA0832 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62509 #2: Chemical | ChemComp-DES / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.06 % |
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Crystal grow | Temperature: 297 K / pH: 8 Details: PEG3350, NaOAc, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2002 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→45 Å / Num. obs: 57942 / % possible obs: 99 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.039 / Net I/σ(I): 46.6 |
Reflection shell | Resolution: 2.13→2.21 Å / Mean I/σ(I) obs: 9.7 / Rsym value: 0.159 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KV6 Resolution: 2.13→29.3 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 768655.75 / Data cutoff high rms absF: 768655.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.1 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.13→29.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.21 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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