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Yorodumi- PDB-6keo: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6keo | ||||||||||||
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Title | Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in 17beta-estradiol-bound form | ||||||||||||
Components | Glutathione S-transferase E14 | ||||||||||||
Keywords | TRANSFERASE / Glutathione / Glutathione S-transferase / GST | ||||||||||||
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: 1.7 Å | ||||||||||||
Authors | Koiwai, K. / Inaba, K. / Morohashi, K. / Yumoto, F. / Niwa, R. / Senda, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: An integrated approach to unravel a crucial structural property required for the function of the insect steroidogenic Halloween protein Noppera-bo. Authors: Koiwai, K. / Inaba, K. / Morohashi, K. / Enya, S. / Arai, R. / Kojima, H. / Okabe, T. / Fujikawa, Y. / Inoue, H. / Yoshino, R. / Hirokawa, T. / Kato, K. / Fukuzawa, K. / Shimada-Niwa, Y. / ...Authors: Koiwai, K. / Inaba, K. / Morohashi, K. / Enya, S. / Arai, R. / Kojima, H. / Okabe, T. / Fujikawa, Y. / Inoue, H. / Yoshino, R. / Hirokawa, T. / Kato, K. / Fukuzawa, K. / Shimada-Niwa, Y. / Nakamura, A. / 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 | 6keo.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6keo.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6keo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6keo_validation.pdf.gz | 953.5 KB | Display | wwPDB validaton report |
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Full document | 6keo_full_validation.pdf.gz | 974.1 KB | Display | |
Data in XML | 6keo_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 6keo_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6keo ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6keo | HTTPS FTP |
-Related structure data
Related structure data | 6kelC 6kemSC 6kenC 6kepC 6keqC 6kerC 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7JYX0, glutathione transferase #2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | Authors state that the conflicts are due to natural valiant. | |
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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: 2.34 Å3/Da / Density % sol: 47.39 % / Description: orthorhombic |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 42.5%(v/v) PPG400, 100mM Bis-Tris, and pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen gas flow / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2015 |
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: 1.58→35.49 Å / Num. obs: 57956 / % possible obs: 87.3 % / Redundancy: 14.1 % / Biso Wilson estimate: 20.79 Å2 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.0495 / Net I/σ(I): 37.59 |
Reflection shell | Resolution: 1.58→1.636 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.8401 / Mean I/σ(I) obs: 2.61 / Num. unique obs: 3057 / Rrim(I) all: 0.8835 / % possible all: 46.64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KEM Resolution: 1.7→35.49 Å / SU ML: 0.2124 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0817 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: 24.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.49 Å
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Refine LS restraints |
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LS refinement shell |
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