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- PDB-8q8b: Crystal structure of Apis mellifera glutathione transferase delta... -

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Basic information

Entry
Database: PDB / ID: 8q8b
TitleCrystal structure of Apis mellifera glutathione transferase delta 1, mutant C127S
ComponentsGlutathione S-transferase D1 isoform X1
KeywordsTRANSFERASE / glutathione transferase / detoxification
Function / homology
Function and homology information


glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase D1 isoform X1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSchwartz, M. / Neiers, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Febs Lett. / Year: 2023
Title: Structure-activity analysis suggests an olfactory function for the unique antennal delta glutathione transferase of Apis mellifera.
Authors: Schwartz, M. / Boichot, V. / Muradova, M. / Fournier, P. / Senet, P. / Nicolai, A. / Canon, F. / Lirussi, F. / Ladeira, R. / Maibeche, M. / Chertemps, T. / Aubert, E. / Didierjean, C. / Neiers, F.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Revision 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase D1 isoform X1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1663
Polymers24,9741
Non-polymers1922
Water3,315184
1
A: Glutathione S-transferase D1 isoform X1
hetero molecules

A: Glutathione S-transferase D1 isoform X1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3326
Polymers49,9482
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3060 Å2
ΔGint-76 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.398, 77.398, 82.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-506-

HOH

31A-556-

HOH

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Components

#1: Protein Glutathione S-transferase D1 isoform X1


Mass: 24973.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: 409490, Gst1, GstD1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7M7GUY7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.5→45.54 Å / Num. obs: 40123 / % possible obs: 99.1 % / Redundancy: 13.2 % / Biso Wilson estimate: 24.03 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Net I/σ(I): 21.4
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.572 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1923 / CC1/2: 0.859 / Rpim(I) all: 0.435 / Rrim(I) all: 1.632

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→36.28 Å / SU ML: 0.1881 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2402 2111 5.27 %
Rwork0.2094 37912 -
obs0.211 40023 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 10 185 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571704
X-RAY DIFFRACTIONf_angle_d0.84262304
X-RAY DIFFRACTIONf_chiral_restr0.0542244
X-RAY DIFFRACTIONf_plane_restr0.0055294
X-RAY DIFFRACTIONf_dihedral_angle_d14.2609637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.33631140.30812468X-RAY DIFFRACTION97.84
1.53-1.570.26211480.2852446X-RAY DIFFRACTION97.74
1.57-1.620.29471410.25992469X-RAY DIFFRACTION98.12
1.62-1.660.25371440.24742469X-RAY DIFFRACTION98.05
1.66-1.720.26091280.26432489X-RAY DIFFRACTION98.05
1.72-1.780.25351370.2542478X-RAY DIFFRACTION98.6
1.78-1.850.30551650.23472497X-RAY DIFFRACTION98.81
1.85-1.930.27181570.22422467X-RAY DIFFRACTION99.02
1.93-2.040.2691360.22342553X-RAY DIFFRACTION99.19
2.04-2.160.251350.22132506X-RAY DIFFRACTION98.14
2.16-2.330.26031200.21312573X-RAY DIFFRACTION99.63
2.33-2.560.23891320.21372577X-RAY DIFFRACTION99.67
2.57-2.940.25271570.21682568X-RAY DIFFRACTION99.85
2.94-3.70.23121450.19382607X-RAY DIFFRACTION99.14
3.7-36.280.20731520.18582745X-RAY DIFFRACTION98.94

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