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- PDB-9ddl: Glutathione transferase sigma class from Taenia solium 1.3 -

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Basic information

Entry
Database: PDB / ID: 9ddl
TitleGlutathione transferase sigma class from Taenia solium 1.3
ComponentsSigma-type glutathione S-transferase
KeywordsTRANSFERASE / Glutathione transferase / Prostaglandine D2 syntase / Glutathione transferase sigma class / Taenia solium
Function / homology
Function and homology information


glutathione transferase activity / glutathione metabolic process
Similarity search - Function
Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal / 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
DI(HYDROXYETHYL)ETHER / Sigma-type glutathione S-transferase
Similarity search - Component
Biological speciesTaenia solium (pork tapeworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMiranda-Blancas, R. / Cardona-Echavarria, M.C. / Sanchez, C. / Sanchez-Perez, L.C. / Flores-Lopez, R. / Rodriguez-Lima, O. / Garcia-Gutierrez, P. / Zubillaga, R. / Landa, A. / Rudino-Pinera, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Not funded Mexico
CitationJournal: Plos Negl Trop Dis / Year: 2025
Title: Structural insights into sigma class glutathione transferase from Taenia solium: Analysis and functional implications.
Authors: Miranda-Blancas, R. / Garcia-Gutierrez, P. / Sanchez-Juarez, C. / Cardona-Echavarria, M.C. / Flores-Lopez, R. / Zubillaga, R.A. / Rodriguez-Lima, O. / Sanchez-Perez, L.C. / Rudino-Pinera, E. / Landa, A.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sigma-type glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4332
Polymers24,3261
Non-polymers1061
Water3,387188
1
A: Sigma-type glutathione S-transferase
hetero molecules

A: Sigma-type glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8654
Polymers48,6532
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2380 Å2
ΔGint-9 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.020, 111.300, 65.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-586-

HOH

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Components

#1: Protein Sigma-type glutathione S-transferase


Mass: 24326.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taenia solium (pork tapeworm) / Gene: GST-28 / Production host: Escherichia coli (E. coli) / References: UniProt: C0M0N5
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 43.02 %
Crystal growTemperature: 291.15 K / Method: microbatch / pH: 7.4 / Details: Tris 50 mM Sodium citrate 100 mM / PH range: 5.8-74

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2023 / Details: Si 111 double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.3→31.1 Å / Num. obs: 50886 / % possible obs: 98.97 % / Redundancy: 13.1 % / Biso Wilson estimate: 15.9 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.014 / Rrim(I) all: 0.055 / Net I/σ(I): 20.96
Reflection shellResolution: 1.3→1.34 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.64 / Num. unique obs: 4964 / CC1/2: 0.88 / CC star: 0.97 / Rpim(I) all: 0.26 / Rrim(I) all: 0.95 / % possible all: 97.85

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→31.1 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 2588 5.09 %
Rwork0.1885 --
obs0.1902 50885 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 7 188 1832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.946
X-RAY DIFFRACTIONf_dihedral_angle_d5.962270
X-RAY DIFFRACTIONf_chiral_restr0.078287
X-RAY DIFFRACTIONf_plane_restr0.008336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.4281400.37762619X-RAY DIFFRACTION98
1.33-1.350.37841360.35112617X-RAY DIFFRACTION98
1.35-1.380.32441422636X-RAY DIFFRACTION98
1.38-1.410.34311310.30562630X-RAY DIFFRACTION98
1.41-1.450.32091540.29722648X-RAY DIFFRACTION98
1.45-1.490.32181460.26712629X-RAY DIFFRACTION99
1.49-1.530.28211520.24722640X-RAY DIFFRACTION99
1.53-1.580.25571390.22312652X-RAY DIFFRACTION99
1.58-1.640.20051380.19972686X-RAY DIFFRACTION99
1.64-1.70.25491370.21392674X-RAY DIFFRACTION99
1.7-1.780.23041580.19782660X-RAY DIFFRACTION99
1.78-1.870.21631360.18482676X-RAY DIFFRACTION100
1.87-1.990.21161300.17612720X-RAY DIFFRACTION100
1.99-2.150.2141480.16872700X-RAY DIFFRACTION100
2.15-2.360.1871370.16052730X-RAY DIFFRACTION100
2.36-2.70.19391470.17192737X-RAY DIFFRACTION100
2.7-3.410.1931670.1682750X-RAY DIFFRACTION100
3.41-100.21461500.16472893X-RAY DIFFRACTION100

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