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Yorodumi- PDB-6keq: Crystal structure of D113A mutant of Drosophila melanogaster Nopp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6keq | ||||||||||||
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Title | Crystal structure of D113A mutant of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in apo-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: 1.84 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 | 6keq.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6keq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6keq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6keq_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 6keq_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 6keq_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6keq_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6keq ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6keq | HTTPS FTP |
-Related structure data
Related structure data | 6kelC 6kemSC 6kenC 6keoC 6kepC 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: 27499.756 Da / Num. of mol.: 2 / Mutation: D113A 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: Water | ChemComp-HOH / | 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: 2.33 Å3/Da / Density % sol: 47.2 % / 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, 100 mM Bis-Tris, and 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-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 29, 2018 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.838→46.34 Å / Num. obs: 42116 / % possible obs: 99.82 % / Redundancy: 13.3 % / Biso Wilson estimate: 31.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.02 / Rrim(I) all: 0.075 / Net I/σ(I): 21.31 |
Reflection shell | Resolution: 1.838→1.904 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 4095 / CC1/2: 0.837 / Rpim(I) all: 0.306 / Rrim(I) all: 1.141 / % possible all: 98.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KEM Resolution: 1.84→46.34 Å / SU ML: 0.2525 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6499 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: 33.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→46.34 Å
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Refine LS restraints |
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LS refinement shell |
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