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- PDB-6tlt: ROR(gamma)t ligand binding domain in complex with desmosterol and... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tlt | ||||||||||||
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Title | ROR(gamma)t ligand binding domain in complex with desmosterol and allosteric ligand Glenmark | ||||||||||||
![]() | Nuclear receptor ROR-gamma | ||||||||||||
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Function / homology | ![]() T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | de Vries, R.M.J.M. / Meijer, F.A. / Brunsveld, L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cooperativity between the orthosteric and allosteric ligand binding sites of ROR gamma t. Authors: de Vries, R.M.J.M. / Meijer, F.A. / Doveston, R.G. / Leijten-van de Gevel, I.A. / Brunsveld, L. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.4 KB | Display | ![]() |
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PDB format | ![]() | 93.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6t4gC ![]() 6t4iC ![]() 6t4jC ![]() 6t4kC ![]() 6t4tC ![]() 6t4uC ![]() 6t4wC ![]() 6t4xC ![]() 6t4yC ![]() 6t50C ![]() 6tlqC ![]() 6salS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 30514.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MJE / |
#3: Chemical | ChemComp-MHQ / ![]() |
#4: Chemical | ChemComp-GOL / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.6M AmSO4 + 0.1M Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→94.16 Å / Num. obs: 28545 / % possible obs: 99.4 % / Redundancy: 37.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.041 / Rrim(I) all: 0.252 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 1611 / CC1/2: 0.414 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6SAL Resolution: 2.11→70.022 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.66 Å2 / Biso mean: 65.8235 Å2 / Biso min: 31.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.11→70.022 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 5.6555 Å / Origin y: -39.8701 Å / Origin z: -4.9238 Å
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Refinement TLS group | Selection details: (chain A and resseq 268:603) |