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Yorodumi- PDB-7db2: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7db2 | ||||||||||||
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Title | Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in GS-dimedone-bound form | ||||||||||||
Components | Glutathione S-transferase E14 | ||||||||||||
Keywords | TRANSFERASE / Drosophila melanogaster / Glutathione S-transferase / GST / GSTE14 / Inhibitor / Ecdysteroid | ||||||||||||
Function / homology | Function and homology information 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 | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Koiwai, K. / Inaba, K. / Yumoto, F. / Senda, T. / Niwa, R. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J Pestic Sci / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7db2.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7db2.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 7db2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7db2_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7db2_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7db2_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 7db2_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/7db2 ftp://data.pdbj.org/pub/pdb/validation_reports/db/7db2 | HTTPS FTP |
-Related structure data
Related structure data | 7daxC 7dayC 7dazC 7db0C 7db1C 7db3C 7db4C 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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1 |
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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.) Drosophila melanogaster (fruit fly) / Gene: GstE14, GSTD14-14, nobo, CG4688 / Plasmid: pCOLD_III / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7JYX0, glutathione transferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Nonpolymer details | Linked ligands DC1+GSH were chemically synthesized as glutathionylated dimedone (GS-dimedone). | |
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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: 2.15 Å3/Da / Density % sol: 42.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / 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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 15, 2018 |
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: 1.4→34.944 Å / Num. obs: 93907 / % possible obs: 99.98 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Biso Wilson estimate: 20.257597051 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0448 / Rrim(I) all: 0.0467 / Net I/σ(I): 29.12 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.0448 / Num. unique obs: 9280 / CC1/2: 0.835 / CC star: 0.954 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KEM Resolution: 1.4→34.94 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→34.94 Å
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Refine LS restraints |
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LS refinement shell |
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