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- PDB-7ebu: Crystal structure of Aedes aegypti Noppera-bo, glutathione S-tran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ebu | ||||||||||||
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Title | Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in Daidzein- and glutathione-bound form | ||||||||||||
![]() | Glutathione transferase | ||||||||||||
![]() | TRANSFERASE / Glutathione / Glutathione S-transferase / GST | ||||||||||||
Function / homology | ![]() glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Inaba, K. / Koiwai, K. / Senda, M. / Senda, T. / Niwa, R. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti. Authors: Inaba, K. / Ebihara, K. / Senda, M. / Yoshino, R. / Sakuma, C. / Koiwai, K. / Takaya, D. / Watanabe, C. / Watanabe, A. / Kawashima, Y. / Fukuzawa, K. / Imamura, R. / Kojima, H. / Okabe, T. / ...Authors: Inaba, K. / Ebihara, K. / Senda, M. / Yoshino, R. / Sakuma, C. / Koiwai, K. / Takaya, D. / Watanabe, C. / Watanabe, A. / Kawashima, Y. / Fukuzawa, K. / Imamura, R. / Kojima, H. / Okabe, T. / Uemura, N. / Kasai, S. / Kanuka, H. / Nishimura, T. / Watanabe, K. / Inoue, H. / Fujikawa, Y. / Honma, T. / Hirokawa, T. / 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 | ![]() | 223.8 KB | Display | ![]() |
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PDB format | ![]() | 161 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ebtC ![]() 7ebvC ![]() 7ebwC ![]() 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26069.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: A0A1S4FIB3 #2: Chemical | ChemComp-GSH / #3: Chemical | ChemComp-ZF1 / #4: Chemical | ChemComp-CA / #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: 2.04 Å3/Da / Density % sol: 39.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 32.5%(w/v) PEG 4000, 0.5 M CaCl2, 0.1 M Tris-HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.13 Å / Num. obs: 62167 / % possible obs: 99.5 % / Redundancy: 26.5 % / Biso Wilson estimate: 26.11 Å2 / Rpim(I) all: 0.025 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 4293 / Rpim(I) all: 0.235 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6KEM Resolution: 1.95→48.13 Å / SU ML: 0.2495 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8628 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: 28.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→48.13 Å
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Refine LS restraints |
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LS refinement shell |
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