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

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Basic information

Entry
Database: PDB / ID: 7dax
TitleCrystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in TDP013-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
Chem-H1X / Glutathione S-transferase E14
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70000976227 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)56,3228
Polymers55,0882
Non-polymers1,2346
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-24 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.696, 75.069, 108.253
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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-H1X / 2-[(5-tert-butyl-2-methyl-phenyl)sulfonylamino]benzoic acid


Mass: 347.429 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.18 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 34% (v/v) PPG 400, 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: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→31.6218017005 Å / Num. obs: 53049 / % possible obs: 99.46 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 17.63 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0337 / Rrim(I) all: 0.365 / Net I/σ(I): 36.69
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.1828 / Mean I/σ(I) obs: 7.94 / Num. unique obs: 5007 / CC1/2: 0.973 / CC star: 0.993 / % possible all: 95.77

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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: 1.70000976227→31.6218017005 Å / SU ML: 0.141159289679 / Cross valid method: FREE R-VALUE / σ(F): 1.35268350705 / Phase error: 18.5483246859
RfactorNum. reflection% reflection
Rfree0.199069133595 2676 5.04477330568 %
Rwork0.167536896626 50369 -
obs0.169107160218 53045 99.4711872035 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.43528988 Å2
Refinement stepCycle: LAST / Resolution: 1.70000976227→31.6218017005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3515 0 81 438 4034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007467940331983776
X-RAY DIFFRACTIONf_angle_d1.279728626645144
X-RAY DIFFRACTIONf_chiral_restr0.0444770419302567
X-RAY DIFFRACTIONf_plane_restr0.00640122102376660
X-RAY DIFFRACTIONf_dihedral_angle_d14.04111690731378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.70000976227-1.73090.2220511087451360.1987722691612450X-RAY DIFFRACTION94.6905895276
1.7309-1.76420.2436356374421420.1892648655272556X-RAY DIFFRACTION97.2252252252
1.7642-1.80020.2331539320251390.1892831871312631X-RAY DIFFRACTION99.8198198198
1.8002-1.83940.2206242341861450.1867394283372622X-RAY DIFFRACTION99.9638728324
1.8394-1.88210.219582284311400.1792492147712620X-RAY DIFFRACTION99.9637812387
1.8821-1.92920.2313697403551460.1815764709312637X-RAY DIFFRACTION100
1.9292-1.98140.2248470226331460.1796845917122635X-RAY DIFFRACTION100
1.9814-2.03960.2084113992341410.1827107179462628X-RAY DIFFRACTION100
2.0396-2.10550.2111558339581340.1720770415732649X-RAY DIFFRACTION100
2.1055-2.18070.207245302331340.1651738528832670X-RAY DIFFRACTION100
2.1807-2.2680.2094082805151260.1697807979742672X-RAY DIFFRACTION100
2.268-2.37120.1899366335491340.1686310350932654X-RAY DIFFRACTION100
2.3712-2.49610.1904321286891280.1707826910292659X-RAY DIFFRACTION100
2.4961-2.65250.2157394919491360.1711750072462670X-RAY DIFFRACTION100
2.6525-2.85710.2143795453161450.1728295576932683X-RAY DIFFRACTION100
2.8571-3.14440.2016600358711670.1695523841022669X-RAY DIFFRACTION100
3.1444-3.59890.1775376096181550.1593931859692694X-RAY DIFFRACTION100
3.5989-4.53210.1644695061741300.1363120916572763X-RAY DIFFRACTION99.9654457498
4.5321-31.62180170050.1898160987061520.1730251584572807X-RAY DIFFRACTION98.3056478405

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