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Yorodumi- PDB-7ebv: Crystal structure of Aedes aegypti Noppera-bo, glutathione S-tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ebv | ||||||||||||
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Title | Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in luteolin- and glutathione-bound form | ||||||||||||
Components | Glutathione transferase | ||||||||||||
Keywords | TRANSFERASE / Glutathione / Glutathione S-transferase / GST | ||||||||||||
Function / homology | Function and homology information glutathione transferase / glutathione transferase activity / glutathione metabolic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Aedes aegypti (yellow fever mosquito) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||||||||
Authors | Inaba, K. / Koiwai, K. / Senda, M. / Senda, T. / Niwa, R. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Bmc Biol. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ebv.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ebv.ent.gz | 164.2 KB | Display | PDB format |
PDBx/mmJSON format | 7ebv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ebv_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7ebv_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7ebv_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 7ebv_validation.cif.gz | 62 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebv ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebv | HTTPS FTP |
-Related structure data
Related structure data | 7ebtC 7ebuC 7ebwC 6kemS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Aedes aegypti (yellow fever mosquito) / Gene: 5569853 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1S4FIB3 #2: Chemical | ChemComp-GSH / #3: Chemical | ChemComp-LU2 / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.97 Å / Num. obs: 135343 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 18.49 Å2 / Rpim(I) all: 0.013 / Net I/σ(I): 32.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 6625 / Rpim(I) all: 0.275 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KEM Resolution: 1.5→36.69 Å / SU ML: 0.1468 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2477 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: 24.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→36.69 Å
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Refine LS restraints |
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LS refinement shell |
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