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- PDB-9c0a: Sigma class glutathione transferase from Taenia solium 1.75 A -

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Basic information

Entry
Database: PDB / ID: 9c0a
TitleSigma class glutathione transferase from Taenia solium 1.75 A
ComponentsSigma-type glutathione S-transferase
KeywordsIMMUNE SYSTEM / Glutathione / Glutathione transferase Sigma class / Taenia solium / Detoxification system.
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMiranda-Blancas, R. / Cardona-Echavarria, M.C. / Garcia-Gutierrez, P. / Sanchez-Juarez, C. / Flores-Lopez, R. / Zubillaga, R. / Rodriguez-Lima, O. / Sanchez-Perez, L.C. / Landa, A. / Rudino-Pinera, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Not funded Mexico
Citation
Journal: 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.
#1: Journal: Journal of the Mexican Chemical Society / Year: 2025
Title: Effect of Glutathione on the Stability, Dynamics and Catalysis of Two Different Classes of Glutathione Transferases from Taenia solium
Authors: Sanchez-Juarez, C. / Sanchez-Perez, L.C. / Zubillaga, R. / Flores-Lopez, R. / Landa, A. / Jimenez, L. / Miranda-Blancas, R. / Rudino-Pinera, E. / Cardona-Echavarria, M.C. / Garcia-Gutierrez, P.
History
DepositionMay 24, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,9537
Polymers24,3261
Non-polymers6276
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.675, 110.113, 65.454
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-513-

HOH

21A-530-

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
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.8 / Details: Sodium cirtate 1M / PH range: 4.5-5-0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→32.73 Å / Num. obs: 21048 / % possible obs: 99.49 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0307 / Rpim(I) all: 0.0307 / Rrim(I) all: 0.0435 / Net I/σ(I): 32.06
Reflection shellResolution: 1.75→32.73 Å / Rmerge(I) obs: 0.3548 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 2049 / CC1/2: 0.82 / Rpim(I) all: 0.3548 / Rrim(I) all: 0.5017 / % possible all: 98.51

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→32.73 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 -5 %
Rwork0.1891 --
obs0.191 21048 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 41 131 1878
Refine LS restraintsType: f_plane_restr / Dev ideal: 0.006 / Number: 321
LS refinement shellResolution: 1.75→1.81 Å /
Num. reflection% reflection
Rwork3958 -
obs-98.51 %

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