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Yorodumi- PDB-7day: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -
+Open data
-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 | ||||||||||||
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: 1.48 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 | 7day.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7day.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 7day.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7day_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7day_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7day_validation.xml.gz | 25.1 KB | Display | |
Data in CIF | 7day_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7day ftp://data.pdbj.org/pub/pdb/validation_reports/da/7day | 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 (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 | ChemComp-DTT / | #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: 2.17 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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