+Open data
-Basic information
Entry | Database: PDB / ID: 3ixp | ||||||
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Title | Crystal structure of the ecdysone receptor bound to BYI08346 | ||||||
Components |
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Keywords | TRANSCRIPTION / anti-parallel alpha-helices / Transcription regulation | ||||||
Function / homology | Function and homology information ecdysone binding / ecdysone receptor signaling pathway / nuclear steroid receptor activity / nuclear receptor activity / sequence-specific DNA binding / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | Heliothis virescens (tobacco budworm) Helicoverpa armigera (cotton bollworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Moras, D. / Billas, I.M.L. / Browning, C. | ||||||
Citation | Journal: To be Published Title: Adaptability of the ecdysone receptor bound to synthetic ligands Authors: Moras, D. / Billas, I.M.L. / Browning, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ixp.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ixp.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ixp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ixp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3ixp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ixp_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 3ixp_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ixp ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ixp | HTTPS FTP |
-Related structure data
Related structure data | 1r20S 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: 29951.760 Da / Num. of mol.: 1 / Fragment: residues 3-264 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Heliothis virescens (tobacco budworm) / Gene: ecr / Plasmid: pET28b / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIF6 |
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#2: Protein | Mass: 30206.619 Da / Num. of mol.: 1 / Fragment: residues 285-532 / Mutation: W303Y,A361S,L456S,C483S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicoverpa armigera (cotton bollworm) / Gene: usp / Plasmid: pACYC11b / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B9UCQ4 |
#3: Chemical | ChemComp-EPH / |
#4: Chemical | ChemComp-834 / |
#5: 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: 3.14 Å3/Da / Density % sol: 60.78 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 1000, PEG 8000, MgCl2 , Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. all: 17811 / Num. obs: 17801 / Redundancy: 7.5 % / Biso Wilson estimate: 75.2 Å2 / Rsym value: 0.054 / Net I/σ(I): 39.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R20 Resolution: 2.85→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 32.532 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.54 Å2 / Biso mean: 52.164 Å2 / Biso min: 17.07 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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Refine LS restraints |
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Xplor file |
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