[English] 日本語
Yorodumi- PDB-2zas: Crystal structure of human estrogen-related receptor gamma ligand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zas | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with 4-alpha-cumylphenol, a bisphenol A derivative | ||||||
Components | Estrogen-related receptor gamma | ||||||
Keywords | TRANSCRIPTION / ERR gamma / BPA / 4-alpha-cumylphenol / nuclear receptor / Activator / DNA-binding / Metal-binding / Nucleus / Transcription regulation / Zinc-finger | ||||||
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: 2 Å | ||||||
Authors | Matsushima, A. / Kakuta, Y. / Teramoto, T. / Shimohigashi, Y. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2008 Title: ERRgamma tethers strongly bisphenol A and 4-alpha-cumylphenol in an induced-fit manner Authors: Matsushima, A. / Teramoto, T. / Okada, H. / Liu, X. / Tokunaga, T. / Kakuta, Y. / Shimohigashi, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zas.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zas.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zas_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2zas_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 2zas_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 2zas_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/2zas ftp://data.pdbj.org/pub/pdb/validation_reports/za/2zas | HTTPS FTP |
-Related structure data
Related structure data | 2zbsC 2e2rS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27611.137 Da / Num. of mol.: 1 / Fragment: ligand binding domain, UNP residues 222-459 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62508 |
---|---|
#2: Chemical | ChemComp-1OH / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Sequence details | THIS DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.32 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05M HEPES, 0.75M sodium citrate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.8 Å / Num. all: 19919 / Num. obs: 19919 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1948 / Rsym value: 0.705 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E2R Resolution: 2→37.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.721 / SU ML: 0.107 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.056 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→37.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.997→2.049 Å / Total num. of bins used: 20
|