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- PDB-7day: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7day | ||||||||||||
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Title | Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in TDP013-, and GSH-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 | ![]() | 130.7 KB | Display | ![]() |
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PDB format | ![]() | 90 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7daxC ![]() 7dazC ![]() 7db0C ![]() 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 | #4: Chemical | ChemComp-DTT / | #5: 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: 2.17 Å3/Da / Density % sol: 43.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 34% (v/v) PPG400 in 80 mM 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: Dec 18, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→37.55 Å / Num. obs: 80334 / % possible obs: 99.73 % / Observed criterion σ(I): 2 / Redundancy: 35.7 % / Biso Wilson estimate: 15.67 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.019 / Rrim(I) all: 0.119 / Net I/σ(I): 27.07 |
Reflection shell | Resolution: 1.48→1.533 Å / Redundancy: 20.1 % / Rmerge(I) obs: 0.9813 / Mean I/σ(I) obs: 3.98 / Num. unique obs: 7800 / CC1/2: 0.841 / CC star: 0.956 / Rpim(I) all: 0.2182 / Rrim(I) all: 1.007 / % possible all: 97.83 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KEM Resolution: 1.48→37.55 Å / SU ML: 0.1507 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.7606 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: 22.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→37.55 Å
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Refine LS restraints |
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LS refinement shell |
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