+Open data
-Basic information
Entry | Database: PDB / ID: 2qnv | ||||||
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Title | Crystal Structure of the Pregnane X Receptor bound to Colupulone | ||||||
Components | Orphan nuclear receptor PXR | ||||||
Keywords | NUCLEAR PROTEIN / Alpha Helical Sandwhich / Protein-Ligand complex / Alternative splicing / DNA-binding / Metal-binding / Nucleus / Polymorphism / Receptor / Transcription / Transcription regulation / Zinc-finger | ||||||
Function / homology | Function and homology information xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...xenobiotic transport / intermediate filament cytoskeleton / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Teotico, D.G. / Bischof, J. / Redinbo, M.R. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of the Pregnane X Receptor bound to Colupulone Authors: Teotico, D.G. / Bischof, J. / Redinbo, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qnv.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qnv.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/2qnv ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qnv | HTTPS FTP |
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-Related structure data
Related structure data | 1ilhS 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: 36280.867 Da / Num. of mol.: 1 / Fragment: PXR Ligand Binding Domain; residues 130-434 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75469 |
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#2: Chemical | ChemComp-CDZ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Precipitant: 10% Isopropanol; Cryoprotectant: done by serial dipping into 15%, 25% and 35% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 70 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5418 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2005 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 8870 / Num. obs: 8870 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 48.1 Å2 / Rsym value: 0.105 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1166 / Rsym value: 0.435 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ILH Resolution: 2.8→45.43 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 366878.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.399 Å2 / ksol: 0.371369 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→45.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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