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- PDB-7db0: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7db0 | ||||||||||||
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Title | Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in dimedone-bound form | ||||||||||||
![]() | Glutathione S-transferase E14 | ||||||||||||
![]() | TRANSFERASE / Drosophila melanogaster / Glutathione S-transferase / GST / GSTE14 / Inhibitor / Ecdysteroid | ||||||||||||
Function / homology | ![]() ecdysteroid biosynthetic process / steroid delta-isomerase activity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cholesterol homeostasis / response to toxic substance / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Koiwai, K. / Inaba, K. / Yumoto, F. / Senda, T. / Niwa, R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo Authors: Koiwai, K. / Morohashi, K. / Inaba, K. / Ebihara, K. / Kojima, H. / Okabe, T. / Yoshino, R. / Hirokawa, T. / Nampo, T. / Fujikawa, Y. / Inoue, H. / Yumoto, F. / Senda, T. / Niwa, R. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 92.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7daxC ![]() 7dayC ![]() 7dazC ![]() 7db1C ![]() 7db2C ![]() 7db3C ![]() 7db4C ![]() 6kemS S: Starting model for refinement C: citing same article ( |
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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: 27543.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-DMS / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 34% (v/v) PPG400 in 80mM Bis-Tris, pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 14, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→35.39 Å / Num. obs: 56430 / % possible obs: 99.86 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.98 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.057 / Rrim(I) all: 0.128 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.66→1.719 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5570 / CC1/2: 0.721 / CC star: 0.915 / Rpim(I) all: 0.3663 / Rrim(I) all: 0.82 / % possible all: 99.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KEM Resolution: 1.66→35.39 Å / SU ML: 0.1602 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.7195 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→35.39 Å
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Refine LS restraints |
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LS refinement shell |
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