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- PDB-6keo: Crystal structure of Drosophila melanogaster Noppera-bo, glutathi... -

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Basic information

Entry
Database: PDB / ID: 6keo
TitleCrystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in 17beta-estradiol-bound form
ComponentsGlutathione S-transferase E14
KeywordsTRANSFERASE / 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
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
ESTRADIOL / Glutathione S-transferase E14
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKoiwai, K. / Inaba, K. / Morohashi, K. / Yumoto, F. / Niwa, R. / Senda, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)18am0101113j0002 Japan
Japan Society for the Promotion of Science15K14719 Japan
Japan Society for the Promotion of Science18K19163 Japan
CitationJournal: 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
DepositionJul 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 1, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_mon_prot_cis / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _entity.pdbx_mutation / _entity.pdbx_number_of_molecules ..._entity.pdbx_mutation / _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _reflns.B_iso_Wilson_estimate / _struct_ref_seq_dif.details / _struct_site.pdbx_num_residues
Description: Polymer geometry
Details: A coordinate file was revised refined at 1.70 angstrom for refinement resolution.
Provider: author / Type: Coordinate replacement
Revision 2.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Glutathione S-transferase E14
BA: Glutathione S-transferase E14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7545
Polymers55,0882
Non-polymers6673
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, homodimer, gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-10 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.398, 75.080, 109.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7JYX0, glutathione transferase
#2: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsAuthors state that the conflicts are due to natural valiant.

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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: 2.34 Å3/Da / Density % sol: 47.39 % / Description: orthorhombic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 42.5%(v/v) PPG400, 100mM Bis-Tris, and pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen gas flow / 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: 1.58→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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KEM

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1766 3.45 %Random selection
Rwork0.1754 49406 --
obs0.1767 51172 95.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.69 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 48 403 4016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00833839
X-RAY DIFFRACTIONf_angle_d0.96365232
X-RAY DIFFRACTIONf_chiral_restr0.052587
X-RAY DIFFRACTIONf_plane_restr0.0059673
X-RAY DIFFRACTIONf_dihedral_angle_d6.17513143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.30791000.25842789X-RAY DIFFRACTION71.56
1.75-1.80.27071210.23753392X-RAY DIFFRACTION86.83
1.8-1.860.29471360.20953834X-RAY DIFFRACTION97.66
1.86-1.920.23961380.20193851X-RAY DIFFRACTION97.94
1.92-20.22691380.20333838X-RAY DIFFRACTION98.15
2-2.090.25271380.19583885X-RAY DIFFRACTION98.19
2.09-2.20.24771380.18513862X-RAY DIFFRACTION98.55
2.2-2.340.2261410.183919X-RAY DIFFRACTION98.66
2.34-2.520.2061390.17913906X-RAY DIFFRACTION98.95
2.52-2.770.2381410.17933943X-RAY DIFFRACTION99.05
2.77-3.170.20441420.17793980X-RAY DIFFRACTION99.35
3.17-40.18851450.15694022X-RAY DIFFRACTION99.59
4-35.490.16941490.15054185X-RAY DIFFRACTION99.24

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