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Yorodumi- PDB-1g2n: CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE ULTRASPIRAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2n | ||||||
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Title | CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE ULTRASPIRACLE PROTEIN USP, THE ORTHOLOG OF RXRS IN INSECTS | ||||||
Components | ULTRASPIRACLE PROTEIN | ||||||
Keywords | GENE REGULATION / ANTIPARALLEL ALPHA-HELICAL SANDWICH / Structural Proteomics in Europe / SPINE / Structural Genomics | ||||||
Function / homology | Function and homology information nuclear steroid receptor activity / regulation of DNA-templated transcription / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Heliothis virescens (tobacco budworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Billas, I.M.L. / Moulinier, L. / Rochel, N. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Crystal structure of the ligand-binding domain of the ultraspiracle protein USP, the ortholog of retinoid X receptors in insects. Authors: Billas, I.M. / Moulinier, L. / Rochel, N. / Moras, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2n.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2n.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1g2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g2n_validation.pdf.gz | 705.7 KB | Display | wwPDB validaton report |
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Full document | 1g2n_full_validation.pdf.gz | 711.7 KB | Display | |
Data in XML | 1g2n_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 1g2n_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2n ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2n | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29962.717 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Gene: USP LOCUS / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIF6 |
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#2: Chemical | ChemComp-EPH / |
#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: 2.04 Å3/Da / Density % sol: 39.84 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Tris, NaCl, dithiothreitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.966 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2000 / Details: Toroidal mirror |
Radiation | Monochromator: DIAMOND (111) + Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 30676 / Num. obs: 30842 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.63 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 38.16 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.224 / % possible all: 90.9 |
Reflection | *PLUS Num. obs: 30676 |
Reflection shell | *PLUS Mean I/σ(I) obs: 4.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1685615.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.81 Å2 / ksol: 0.337 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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