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Yorodumi- PDB-1r20: Crystal structure of the ligand-binding domains of the heterodime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r20 | ||||||
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Title | Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to the synthetic agonist BYI06830 | ||||||
Components |
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Keywords | hormone/growth factor receptor / NUCLEAR RECEPTOR / HETERODIMER / ALPHA-HELICAL SANDWICH / Structural Proteomics in Europe / SPINE / Structural Genomics / hormone-growth factor receptor COMPLEX | ||||||
Function / homology | Function and homology information ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Heliothis virescens (tobacco budworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Billas, I.M.L. / Iwema, T. / Garnier, J.M. / Mitschler, A. / Rochel, N. / Moras, D. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Nature / Year: 2003 Title: Structural adaptability in the ligand-binding pocket of the ecdysone hormone receptor. Authors: Billas, I.M.L. / Iwema, T. / Garnier, J.M. / Mitschler, A. / Rochel, N. / Moras, D. | ||||||
History |
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Remark 999 | sequence no suitable sequence database reference was available for chains A or D, at the time of ...sequence no suitable sequence database reference was available for chains A or D, at the time of processing this file. In chain D the following residues were mutated compared to the wild- type protein: W303Y, A361S, L456S, C483S. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r20.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r20.ent.gz | 83 KB | Display | PDB format |
PDBx/mmJSON format | 1r20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r20_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1r20_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1r20_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 1r20_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/1r20 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/1r20 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29951.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: pACYC11b / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF6 |
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#2: Protein | Mass: 30206.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: O18473 |
#3: Chemical | ChemComp-EPH / |
#4: Chemical | ChemComp-HWG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.38 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 1000, PEG 8000, MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3→15 Å / Num. all: 15421 / Num. obs: 15421 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rsym value: 0.072 | ||||||||||||||||||
Reflection shell | Resolution: 3→3.07 Å / Rsym value: 0.355 / % possible all: 85.6 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 3 Å / Redundancy: 8.3 % / Num. measured all: 127854 / Rmerge(I) obs: 0.072 | ||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 3 Å / % possible obs: 85.6 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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