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- PDB-7db2: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -

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Basic information

Entry
Database: PDB / ID: 7db2
TitleCrystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in GS-dimedone-bound form
ComponentsGlutathione S-transferase E14
KeywordsTRANSFERASE / 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
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
5,5-DIMETHYLCYCLOHEXANE-1,3-DIONE / GLUTATHIONE / Glutathione S-transferase E14
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKoiwai, K. / Inaba, K. / Yumoto, F. / Senda, T. / Niwa, R.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)18am0101113j0002 Japan
Japan Society for the Promotion of Science (JSPS)15K14719 Japan
Japan Society for the Promotion of Science (JSPS)18K19163 Japan
CitationJournal: 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
DepositionOct 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase E14
B: Glutathione S-transferase E14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1398
Polymers55,0882
Non-polymers1,0516
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-13 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.676, 75.887, 106.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glutathione S-transferase E14 / Protein noppera-bo


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 ChemComp-DC1 / 5,5-DIMETHYLCYCLOHEXANE-1,3-DIONE / 2,2 DIMETHYL,1,6 CYCLOHEXA DIONE / DIMEDONE


Mass: 140.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Nonpolymer detailsLinked ligands DC1+GSH were chemically synthesized as glutathionylated dimedone (GS-dimedone).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 34% (v/v) PPG400 in 80mM Bis-Tris, pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 15, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSJun 17, 2015data reduction
Aimless0.5.15data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KEM

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
RfactorNum. reflection% reflection
Rfree0.2187 4643 4.94 %
Rwork0.1951 --
obs0.1962 93905 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 68 445 4067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063913
X-RAY DIFFRACTIONf_angle_d1.0355328
X-RAY DIFFRACTIONf_dihedral_angle_d13.2361458
X-RAY DIFFRACTIONf_chiral_restr0.065588
X-RAY DIFFRACTIONf_plane_restr0.005703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.3571600.33562949X-RAY DIFFRACTION100
1.4159-1.43260.34141540.32832957X-RAY DIFFRACTION100
1.4326-1.450.35051650.30772895X-RAY DIFFRACTION100
1.45-1.46840.34191450.2962947X-RAY DIFFRACTION100
1.4684-1.48770.32581490.28672938X-RAY DIFFRACTION100
1.4877-1.50810.32051170.27442994X-RAY DIFFRACTION100
1.5081-1.52960.28361490.27232922X-RAY DIFFRACTION100
1.5296-1.55250.29391560.26112979X-RAY DIFFRACTION100
1.5525-1.57670.30841580.25132930X-RAY DIFFRACTION100
1.5767-1.60260.29581540.25362932X-RAY DIFFRACTION100
1.6026-1.63020.29271520.2532991X-RAY DIFFRACTION100
1.6302-1.65990.27431480.2432933X-RAY DIFFRACTION100
1.6599-1.69180.2821330.24282947X-RAY DIFFRACTION100
1.6918-1.72630.28221380.24953008X-RAY DIFFRACTION100
1.7263-1.76390.30321580.24832938X-RAY DIFFRACTION100
1.7639-1.80490.27831620.24492947X-RAY DIFFRACTION100
1.8049-1.850.2531580.24142970X-RAY DIFFRACTION100
1.85-1.90.27841640.23592942X-RAY DIFFRACTION100
1.9-1.95590.22171560.22092989X-RAY DIFFRACTION100
1.9559-2.01910.21261470.22362948X-RAY DIFFRACTION100
2.0191-2.09120.24941630.21082972X-RAY DIFFRACTION100
2.0912-2.17490.22141530.1972993X-RAY DIFFRACTION100
2.1749-2.27390.23671650.19632941X-RAY DIFFRACTION100
2.2739-2.39380.181420.19423005X-RAY DIFFRACTION100
2.3938-2.54370.2241680.19172993X-RAY DIFFRACTION100
2.5437-2.740.20211790.18612991X-RAY DIFFRACTION100
2.74-3.01560.21741560.18442993X-RAY DIFFRACTION100
3.0156-3.45170.19211740.17083036X-RAY DIFFRACTION100
3.4517-4.34740.16561510.14593070X-RAY DIFFRACTION100
4.3474-34.940.18311690.16093212X-RAY DIFFRACTION100

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