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- PDB-5jcu: Crystal Structure of hGSTA1-1 with Glutathione Adduct of Phenethy... -

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Basic information

Entry
Database: PDB / ID: 5jcu
TitleCrystal Structure of hGSTA1-1 with Glutathione Adduct of Phenethyl Isothiocyanate and Cystein Adduct of Phenethyl Isothiocyanate
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / GST / PEITC / Glutathione adduct / Cyctein adduct
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / linoleic acid metabolic process / steroid Delta-isomerase activity / 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 / linoleic acid metabolic process / steroid Delta-isomerase activity / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, alpha class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-GVX / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.93 Å
AuthorsKumari, V. / Ji, X.
Citation
Journal: Plos One / Year: 2016
Title: Irreversible Inhibition of Glutathione S-Transferase by Phenethyl Isothiocyanate (PEITC), a Dietary Cancer Chemopreventive Phytochemical.
Authors: Kumari, V. / Dyba, M.A. / Holland, R.J. / Liang, Y.H. / Singh, S.V. / Ji, X.
#1: Journal: J. Mol. Biol. / Year: 1993
Title: Structure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the Mu and Pi class enzymes.
Authors: Sinning, I. / Kleywegt, G.J. / Cowan, S.W. / Reinemer, P. / Dirr, H.W. / Huber, R. / Gilliland, G.L. / Armstrong, R.N. / Ji, X. / Board, P.G.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_struct_oper_list
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
C: Glutathione S-transferase A1
D: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,06314
Polymers102,8094
Non-polymers2,25510
Water19,6001088
1
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5327
Polymers51,4042
Non-polymers1,1275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-14 kcal/mol
Surface area19900 Å2
MethodPISA
2
C: Glutathione S-transferase A1
D: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5327
Polymers51,4042
Non-polymers1,1275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-14 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.335, 92.666, 104.051
Angle α, β, γ (deg.)90.00, 92.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

21A-554-

HOH

31A-635-

HOH

41C-561-

HOH

51D-577-

HOH

61D-590-

HOH

71D-634-

HOH

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Components

#1: Protein
Glutathione S-transferase A1 / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1


Mass: 25702.166 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pET30b(+)/hGSTA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: P08263, glutathione transferase
#2: Chemical
ChemComp-GVX / L-gamma-glutamyl-S-[(2-phenylethyl)carbamothioyl]-L-cysteinylglycine


Type: peptide-like / Mass: 470.563 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26N4O6S2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1088 / 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: 2.36 Å3/Da / Density % sol: 47.92 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG 3350 20% (w/v), Sodium acetate 0.2 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. obs: 71288 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / CC1/2: 0.695 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.04
Reflection shellResolution: 1.93→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 1.64 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GUH

1guh


Resolution: 1.93→29.799 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.57
RfactorNum. reflection% reflectionSelection details
Rfree0.24 998 1.4 %Random
Rwork0.1772 ---
obs0.1782 71262 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.2 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 148 1088 8464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097588
X-RAY DIFFRACTIONf_angle_d1.0910187
X-RAY DIFFRACTIONf_dihedral_angle_d16.1122995
X-RAY DIFFRACTIONf_chiral_restr0.0441101
X-RAY DIFFRACTIONf_plane_restr0.0051295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9252-2.02670.31221230.25799780X-RAY DIFFRACTION97
2.0267-2.15360.27971520.21999950X-RAY DIFFRACTION99
2.1536-2.31980.28151420.201410013X-RAY DIFFRACTION99
2.3198-2.55320.30121350.198310044X-RAY DIFFRACTION99
2.5532-2.92240.25871440.193610071X-RAY DIFFRACTION99
2.9224-3.68080.26161480.163810141X-RAY DIFFRACTION100
3.6808-29.80210.17841540.145410265X-RAY DIFFRACTION100

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