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- PDB-1osv: STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1osv | ||||||
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Title | STRUCTURAL BASIS FOR BILE ACID BINDING AND ACTIVATION OF THE NUCLEAR RECEPTOR FXR | ||||||
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Function / homology | ![]() response to norepinephrine / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / negative regulation of triglyceride biosynthetic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / regulation of carbohydrate metabolic process ...response to norepinephrine / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Recycling of bile acids and salts / negative regulation of triglyceride biosynthetic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Recycling of bile acids and salts / regulation of carbohydrate metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of glucocorticoid receptor signaling pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mi, L.Z. / Devarakonda, S. / Harp, J.M. / Han, Q. / Pellicciari, R. / Willson, T.M. / Khorasanizadeh, S. / Rastinejad, F. | ||||||
![]() | ![]() Title: Structural Basis for Bile Acid Binding and Activation of the Nuclear Receptor FXR Authors: Mi, L.Z. / Devarakonda, S. / Harp, J.M. / Han, Q. / Pellicciari, R. / Willson, T.M. / Khorasanizadeh, S. / Rastinejad, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.1 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is one of the two subunits in the asymmetric unit - A or B |
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Components
#1: Protein | Mass: 26850.891 Da / Num. of mol.: 2 / Fragment: ligand binding domain (FXR-LBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | ![]() Mass: 1464.664 Da / Num. of mol.: 3 / Fragment: Residues (741-752) / Source method: obtained synthetically Details: The coactivator peptide was synthesized. The sequence of the GRIP is naturally found in Rattus Norvegicus (Norway Rat). References: UniProt: Q61026 #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.31 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000,Ethylene Glycol, PIPES , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2002 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→24.3 Å / Num. all: 26840 / Num. obs: 24908 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 44.2 Å2 / Rsym value: 0.044 / Net I/σ(I): 19.61 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.04 / Rsym value: 0.282 / % possible all: 77.2 |
Reflection | *PLUS Lowest resolution: 24.3 Å / Num. obs: 24427 / % possible obs: 92.8 % / Num. measured all: 99829 / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 77.2 % / Rmerge(I) obs: 0.282 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.8465 Å2 / ksol: 0.320304 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 24.3 Å / % reflection Rfree: 5 % / Rfactor Rfree![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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