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- PDB-9nxw: Crystal Structure of Glutathione S-Transferase Bla g 24 (delta class) -

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Basic information

Entry
Database: PDB / ID: 9nxw
TitleCrystal Structure of Glutathione S-Transferase Bla g 24 (delta class)
ComponentsGlutathione S transferase class delta
KeywordsTRANSFERASE / Glutathione S-Transferase / GST / GSH / German cockroach / allergen
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 / Glutathione transferase family / 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
GLUTATHIONE / Glutathione S transferase class delta
Similarity search - Component
Biological speciesBlattella germanica (German cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsZong, G. / Pedersen, L.C. / Mueller, G.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZICES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES102906 United States
CitationJournal: Clin Exp Allergy / Year: 2026
Title: Reclassification of GST Allergens Based on Their Cross-Reactivity in Two Divergent Cockroach Species.
Authors: Zong, G. / Lozano, A. / Leighton, G.O. / Randall, T. / Pedersen, L.C. / Glesner, J. / Smith, B.R.E. / Acevedo, N. / Schal, C. / Caraballo, L. / Pomes, A. / Zakzuk, J. / Mueller, G.A.
History
DepositionMar 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S transferase class delta
B: Glutathione S transferase class delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,47013
Polymers49,3192
Non-polymers1,15111
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.425, 83.598, 54.920
Angle α, β, γ (deg.)90.000, 106.748, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glutathione S transferase class delta


Mass: 24659.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blattella germanica (German cockroach) / Production host: Escherichia coli (E. coli) / References: UniProt: G8XWV6
#2: Chemical ChemComp-GSH / Glutathione


Type: peptide-like / Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 43.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M CaCl2, 0.1M HEPES pH 7.5, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→32.73 Å / Num. obs: 196885 / % possible obs: 98.58 % / Redundancy: 2 % / Biso Wilson estimate: 18.15 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.2
Reflection shellResolution: 1.33→1.38 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 8264 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→32.72 Å / SU ML: 0.1555 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1962 4578 4.84 %
Rwork0.1738 89971 -
obs0.1749 94549 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.24 Å2
Refinement stepCycle: LAST / Resolution: 1.33→32.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 69 352 3798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443640
X-RAY DIFFRACTIONf_angle_d0.76254955
X-RAY DIFFRACTIONf_chiral_restr0.0623534
X-RAY DIFFRACTIONf_plane_restr0.0067647
X-RAY DIFFRACTIONf_dihedral_angle_d12.17981328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.2677970.26062278X-RAY DIFFRACTION73.19
1.35-1.360.26051150.26252671X-RAY DIFFRACTION88.78
1.36-1.380.26651550.26522948X-RAY DIFFRACTION97.55
1.38-1.390.33151650.26493003X-RAY DIFFRACTION99.78
1.39-1.410.291640.25443020X-RAY DIFFRACTION100
1.41-1.430.24621660.2423020X-RAY DIFFRACTION100
1.43-1.450.24231430.23973061X-RAY DIFFRACTION100
1.45-1.470.23731400.23443052X-RAY DIFFRACTION100
1.47-1.50.27031510.2313003X-RAY DIFFRACTION100
1.5-1.520.26621380.22093072X-RAY DIFFRACTION100
1.52-1.550.2551940.22122987X-RAY DIFFRACTION100
1.55-1.580.21831520.21063053X-RAY DIFFRACTION100
1.58-1.610.22861570.21013023X-RAY DIFFRACTION100
1.61-1.640.26031590.20433036X-RAY DIFFRACTION100
1.64-1.680.22241550.20013052X-RAY DIFFRACTION99.97
1.68-1.710.2091440.19583030X-RAY DIFFRACTION100
1.71-1.760.21051790.20243013X-RAY DIFFRACTION99.97
1.76-1.810.22871370.19563043X-RAY DIFFRACTION99.97
1.81-1.860.2041500.1893074X-RAY DIFFRACTION100
1.86-1.920.21551660.1842979X-RAY DIFFRACTION99.94
1.92-1.990.191490.1863041X-RAY DIFFRACTION99.97
1.99-2.070.23781400.18783078X-RAY DIFFRACTION99.94
2.07-2.160.20691510.18053015X-RAY DIFFRACTION99.94
2.16-2.270.20261460.16723074X-RAY DIFFRACTION99.94
2.27-2.420.19441590.16013075X-RAY DIFFRACTION100
2.42-2.60.19141440.16073043X-RAY DIFFRACTION99.84
2.6-2.860.17141620.16043046X-RAY DIFFRACTION99.78
2.86-3.280.18711550.16463039X-RAY DIFFRACTION99.78
3.28-4.130.16241650.1443063X-RAY DIFFRACTION99.72
4.13-32.720.17141800.15213079X-RAY DIFFRACTION99.69

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