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- PDB-5x8s: Crystal Structure of the mutant Human ROR gamma Ligand Binding Do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x8s | ||||||
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Title | Crystal Structure of the mutant Human ROR gamma Ligand Binding Domain With Ursolic acid. | ||||||
![]() | Nuclear receptor ROR-gamma | ||||||
![]() | TRANSFERASE/INHIBITOR / Inhibitor / Binary Complex / ![]() | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Noguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Adachi, T. | ||||||
![]() | ![]() Title: Ternary complex of human ROR gamma ligand-binding domain, inverse agonist and SMRT peptide shows a unique mechanism of corepressor recruitment Authors: Noguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Hirata, K. / Shiozaki, M. / Hirashima, S. / Kotoku, M. / Yamaguchi, T. / Katsuda, Y. / Steensma, R. / Li, X. / Tao, H. / ...Authors: Noguchi, M. / Nomura, A. / Murase, K. / Doi, S. / Yamaguchi, K. / Hirata, K. / Shiozaki, M. / Hirashima, S. / Kotoku, M. / Yamaguchi, T. / Katsuda, Y. / Steensma, R. / Li, X. / Tao, H. / Tse, B. / Fenn, M. / Babine, R. / Bradley, E. / Crowe, P. / Thacher, S. / Adachi, T. / Kamada, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.5 KB | Display | ![]() |
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PDB format | ![]() | 89.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5x8qC ![]() 5x8uC ![]() 5x8wC ![]() 5x8xC ![]() 3l0lS C: citing same article ( 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: 29898.516 Da / Num. of mol.: 2 / Fragment: UNP residues 261-518 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes pH7.5, 5% PEG4000, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→101.28 Å / Num. obs: 30947 / % possible obs: 100 % / Redundancy: 21.3 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3L0L Resolution: 2.2→101.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.899 / SU B: 5.14 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.102 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→101.28 Å
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Refine LS restraints |
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