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- PDB-3eyb: Structural and functional insights into the ligand binding domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eyb | ||||||
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Title | Structural and functional insights into the ligand binding domain of a non-duplicated RXR from the invertebrate chordate amphioxus | ||||||
![]() | Nuclear hormone receptor RXR | ||||||
![]() | TRANSCRIPTION / Amphioxus / Retinoid X receptor / nuclear receptor / ligand binding / DNA-binding / Metal-binding / Nucleus / Receptor / Transcription regulation / Zinc-finger / Structural Genomics / Structural Proteomics in Europe / SPINE | ||||||
Function / homology | ![]() nuclear steroid receptor activity / sequence-specific DNA binding / DNA-binding transcription factor activity / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tocchini-Valentini, G.D. / Rochel, N. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: Structural and functional insights into the ligand-binding domain of a nonduplicated retinoid X nuclear receptor from the invertebrate chordate amphioxus Authors: Tocchini-Valentini, G.D. / Rochel, N. / Escriva, H. / Germain, P. / Peluso-Iltis, C. / Paris, M. / Sanglier-Cianferani, S. / Van Dorsselaer, A. / Moras, D. / Laudet, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 158 KB | Display | ![]() |
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PDB format | ![]() | 125.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.2 KB | Display | ![]() |
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Full document | ![]() | 443.6 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lbd S: Starting model for refinement |
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Similar structure data |
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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: 24697.746 Da / Num. of mol.: 4 / Fragment: UNP residues 266-484, Ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET15 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.5 M Na acetate, 0.1 M ADA pH=6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: May 1, 2004 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.79→15 Å / Num. all: 22831 / Num. obs: 22831 / % possible obs: 90.34 % / Observed criterion σ(F): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.79→2.89 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.2 / % possible all: 75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LBD ![]() 1lbd Resolution: 2.79→15 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 56.5 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→2.86 Å / Num. reflection obs: 1339 |