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- PDB-8bhe: K141H and S142H double mutant of hGSTA1-1 -

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Basic information

Entry
Database: PDB / ID: 8bhe
TitleK141H and S142H double mutant of hGSTA1-1
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / Thermostability / Glutathione / Detoxification / Catalysis
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / glutathione metabolic process / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.87 Å
AuthorsPapageorgiou, A.C. / Poudel, N.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)871037European Union
CitationJournal: Int J Mol Sci / Year: 2023
Title: A Key Role in Catalysis and Enzyme Thermostability of a Conserved Helix H5 Motif of Human Glutathione Transferase A1-1.
Authors: Chronopoulou, E.G. / Mutabdzija, L. / Poudel, N. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionOct 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glutathione S-transferase A1
A: Glutathione S-transferase A1


Theoretical massNumber of molelcules
Total (without water)51,4602
Polymers51,4602
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-21 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.499, 79.609, 93.679
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 A1 / / 13-hydroperoxyoctadecadienoate peroxidase / Androst-5-ene-3 / 17-dione isomerase / GST HA subunit 1 ...13-hydroperoxyoctadecadienoate peroxidase / Androst-5-ene-3 / 17-dione isomerase / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1


Mass: 25730.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P08263, glutathione transferase, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 17-20% w/v, Na malonate 0.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.87→93.68 Å / Num. obs: 37747 / % possible obs: 95 % / Redundancy: 4.6 % / Biso Wilson estimate: 39.53 Å2 / CC1/2: 1 / Rrim(I) all: 0.048 / Net I/σ(I): 16.9
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 1.5 % / Num. unique obs: 1358 / CC1/2: 0.514 / Rrim(I) all: 1.245 / % possible all: 36.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.87→49.64 Å / SU ML: 0.2305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2395 1906 5.06 %
Rwork0.2007 35771 -
obs0.2027 37677 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.94 Å2
Refinement stepCycle: LAST / Resolution: 1.87→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 0 295 3647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873435
X-RAY DIFFRACTIONf_angle_d1.00864631
X-RAY DIFFRACTIONf_chiral_restr0.0569510
X-RAY DIFFRACTIONf_plane_restr0.0152587
X-RAY DIFFRACTIONf_dihedral_angle_d5.5742456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.3772590.32361070X-RAY DIFFRACTION39.78
1.92-1.970.32091330.31132445X-RAY DIFFRACTION93.61
1.97-2.030.35351320.28652621X-RAY DIFFRACTION98.64
2.03-2.10.30491310.25862657X-RAY DIFFRACTION99.75
2.1-2.170.29631470.2282651X-RAY DIFFRACTION99.86
2.17-2.260.27121450.21222652X-RAY DIFFRACTION99.82
2.26-2.360.2591470.22172665X-RAY DIFFRACTION99.79
2.36-2.490.22831430.21372664X-RAY DIFFRACTION99.82
2.49-2.640.31191280.22612694X-RAY DIFFRACTION99.75
2.64-2.850.28931630.2382657X-RAY DIFFRACTION99.72
2.85-3.130.31251470.22382681X-RAY DIFFRACTION99.58
3.13-3.580.23421260.19072719X-RAY DIFFRACTION99.61
3.58-4.520.19191530.16292739X-RAY DIFFRACTION99.38
4.52-49.640.19621520.18152856X-RAY DIFFRACTION99.34

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