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Yorodumi- PDB-2zkc: Crystal structure of human estrogen-related receptor gamma ligand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zkc | ||||||
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Title | Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol Z | ||||||
Components | Estrogen-related receptor gamma | ||||||
Keywords | TRANSCRIPTION / ERR gamma / BPA / 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 / intracellular steroid hormone receptor 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 / intracellular steroid hormone receptor 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 / chromatin / regulation of DNA-templated transcription / 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: 1.7 Å | ||||||
Authors | Matsushima, A. / Kakuta, Y. / Teramoto, T. / Shimohigashi, Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol Z Authors: Matsushima, A. / Kakuta, Y. / Teramoto, T. / Shimohigashi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zkc.cif.gz | 67.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zkc.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zkc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zkc ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zkc | HTTPS FTP |
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-Related structure data
Related structure data | 2e2rS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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 | ||||
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#2: Chemical | ChemComp-BPZ / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THIS DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
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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 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.93 Å / Num. obs: 31736 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 48.6 / Num. measured all: 446985 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5929 / Rsym value: 0.473 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2E2R Resolution: 1.7→31.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.002 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.478 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→31.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.699→1.743 Å / Total num. of bins used: 20
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