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- PDB-9f7k: Glutathione transferase epsilon 1 from Drosophila melanogaster in... -

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Basic information

Entry
Database: PDB / ID: 9f7k
TitleGlutathione transferase epsilon 1 from Drosophila melanogaster in complex with glutathione
ComponentsGH14654p
KeywordsTRANSFERASE / glutathione / insect / epsilon
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to heat / cytoplasm
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutaredoxin domain profile. / Glutathione S-transferase, C-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
S-Hydroxy-Glutathione / GLUTATHIONE / GH14654p
Similarity search - Component
Biological speciesDrosophila melanogaster American nodavirus SW-2009a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDidierjean, C. / Schwartz, M. / Neiers, F.
Funding support France, 2items
OrganizationGrant numberCountry
Other governmentUniversite de Lorraine
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Biomolecules / Year: 2024
Title: Structural and Thermodynamic Insights into Dimerization Interfaces of Drosophila Glutathione Transferases.
Authors: Schwartz, M. / Petiot, N. / Chaloyard, J. / Senty-Segault, V. / Lirussi, F. / Senet, P. / Nicolai, A. / Heydel, J.M. / Canon, F. / Sonkaria, S. / Khare, V. / Didierjean, C. / Neiers, F.
History
DepositionMay 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GH14654p
B: GH14654p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4188
Polymers49,9732
Non-polymers1,4456
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-31 kcal/mol
Surface area18120 Å2
Unit cell
Length a, b, c (Å)81.038, 82.919, 95.543
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 222 / Label seq-ID: 4 - 222

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein GH14654p / Glutathione S transferase E1 / Glutathione S-transferase


Mass: 24986.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster American nodavirus (ANV) SW-2009a
Gene: GstE1, CT16545, Dmel\CG5164, DmGST-3, DmGSTE1, DmGSTE1-1, GST-3, Gst-3, gst-3, GST-E1, Gst-theta 55F, GST3, Gst3, Gst55F, GSTE1, gstE1, gste1, CG5164, Dmel_CG5164
Production host: Escherichia coli (E. coli) / References: UniProt: Q7KK90, glutathione transferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#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-GS8 / S-Hydroxy-Glutathione


Mass: 323.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v PEG 8000, 100 mM MES pH 6.0 and 200 mM Ca acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.14071 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14071 Å / Relative weight: 1
ReflectionResolution: 1.8→41.46 Å / Num. obs: 60131 / % possible obs: 99.2 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3542 / CC1/2: 0.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→41.459 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.816 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1766 3053 5.077 %
Rwork0.1537 57078 -
all0.155 --
obs-60131 99.685 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.323 Å2-0 Å20 Å2
2--1.067 Å2-0 Å2
3----0.744 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3482 0 94 208 3784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163505
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6595039
X-RAY DIFFRACTIONr_angle_other_deg0.5731.5788103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.37521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71810593
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.80410153
X-RAY DIFFRACTIONr_chiral_restr0.10.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
X-RAY DIFFRACTIONr_nbd_refined0.220.2737
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.22890
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21811
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21866
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2179
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0850.21
X-RAY DIFFRACTIONr_nbd_other0.1330.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.26
X-RAY DIFFRACTIONr_mcbond_it2.8882.7041778
X-RAY DIFFRACTIONr_mcbond_other2.8742.7041778
X-RAY DIFFRACTIONr_mcangle_it3.6854.8392222
X-RAY DIFFRACTIONr_mcangle_other3.6844.8412223
X-RAY DIFFRACTIONr_scbond_it5.1233.2441913
X-RAY DIFFRACTIONr_scbond_other5.1223.2451914
X-RAY DIFFRACTIONr_scangle_it7.5165.6822811
X-RAY DIFFRACTIONr_scangle_other7.5145.6822812
X-RAY DIFFRACTIONr_lrange_it8.26626.9534156
X-RAY DIFFRACTIONr_lrange_other8.23326.5954117
X-RAY DIFFRACTIONr_ncsr_local_group_10.0720.057406
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.071810.05009
12AX-RAY DIFFRACTIONLocal ncs0.071810.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.2482010.23341920.23443950.960.96299.95450.217
1.847-1.8970.252010.21540870.21742910.9570.96899.93010.197
1.897-1.9520.2252290.20139150.20341590.9670.97199.63930.181
1.952-2.0120.2061890.18338460.18540530.9720.97799.55590.165
2.012-2.0780.2081780.16837880.1739780.9730.98199.69830.149
2.078-2.1510.1762490.14835180.1537670.9810.9861000.132
2.151-2.2310.1481830.13835090.13936920.9880.991000.125
2.231-2.3220.1581650.13333860.13435530.9850.98999.94370.117
2.322-2.4250.1521680.12532370.12634060.9860.99199.97060.112
2.425-2.5430.1411620.1230880.12132500.9880.9911000.108
2.543-2.680.161600.13529570.13631170.9830.991000.124
2.68-2.8420.1761420.14327990.14529420.9840.98999.9660.132
2.842-3.0370.151670.13626060.13727730.9870.991000.129
3.037-3.2790.1631540.14524460.14626080.9830.98899.69330.143
3.279-3.590.1751180.14622930.14824130.9810.98799.91710.148
3.59-4.010.1441130.14320520.14321810.9880.98899.26640.148
4.01-4.6230.162910.1518370.1519430.9870.98899.2280.158
4.623-5.6440.222810.17215510.17416600.9780.98598.31330.186
5.644-7.9090.228590.19912500.213290.9810.98198.49510.213
7.909-41.4590.227430.1637210.1668060.9670.98494.78910.181

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