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- PDB-8z3b: Crystal structure of GSTd2 -

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Basic information

Entry
Database: PDB / ID: 8z3b
TitleCrystal structure of GSTd2
ComponentsGlutathione S-transferase delta
KeywordsTRANSFERASE / Plutella xylostella / Glutathione S-transferase / Molecular cloning / Insecticide resistance
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 / 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 S-transferase delta
Similarity search - Component
Biological speciesPlutella xylostella (diamondback moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMo, X. / Yao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071476 China
CitationJournal: To be published
Title: Characterization of a Plutella xylostella GZTd2, evolved in isothiocyanate detoxification
Authors: Mo, X. / Yao, Y.
History
DepositionApr 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 3, 2024Provider: 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 delta
B: Glutathione S-transferase delta


Theoretical massNumber of molelcules
Total (without water)47,1202
Polymers47,1202
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-19 kcal/mol
Surface area17960 Å2
MethodPISA
2
A: Glutathione S-transferase delta

B: Glutathione S-transferase delta


Theoretical massNumber of molelcules
Total (without water)47,1202
Polymers47,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area2030 Å2
ΔGint-17 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.124, 82.355, 106.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glutathione S-transferase delta


Mass: 23559.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plutella xylostella (diamondback moth) / Gene: PxGSTd / Production host: Escherichia coli (E. coli) / References: UniProt: D7URW9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 15% PEG3350, and 0.12M Tris at a pH of 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25.355 Å / Num. obs: 23353 / % possible obs: 99.77 % / Redundancy: 7.2 % / CC1/2: 0.84 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 2288 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.17.1_360refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.355 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 --
Rwork0.1851 --
obs-23353 99.77 %
Displacement parametersBiso mean: 31.35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 0 254 3582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583404
X-RAY DIFFRACTIONf_angle_d0.93414618
X-RAY DIFFRACTIONf_chiral_restr0.05512
X-RAY DIFFRACTIONf_plane_restr0.0085594
X-RAY DIFFRACTIONf_dihedral_angle_d18.90411250

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