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- PDB-7bib: Crystal structure of human GSTA1-1 bound to the glutathione adduc... -

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Basic information

Entry
Database: PDB / ID: 7bib
TitleCrystal structure of human GSTA1-1 bound to the glutathione adduct of hexyl-isothiocyanate
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / Glutathione transferase / ligandin
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 / epithelial cell differentiation / glutathione metabolic process / 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 / 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, alpha class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
Chem-TZ8 / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSchwartz, M. / Neiers, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Food Chem / Year: 2022
Title: Role of human salivary enzymes in bitter taste perception.
Authors: Schwartz, M. / Brignot, H. / Feron, G. / Hummel, T. / Zhu, Y. / von Koskull, D. / Heydel, J.M. / Lirussi, F. / Canon, F. / Neiers, F.
History
DepositionJan 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,2414
Polymers51,3402
Non-polymers9012
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-21 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.638, 93.222, 51.524
Angle α, β, γ (deg.)90.000, 93.185, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 25670.121 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 (E. coli)
References: UniProt: P08263, glutathione transferase, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds
#2: Chemical ChemComp-TZ8 / (2~{R})-2-azanyl-5-[[(2~{R})-3-(hexylcarbamothioylsulfanyl)-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid


Mass: 450.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H30N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl 0.1M pH 7.5, PEG4000 18%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.03→46.61 Å / Num. obs: 29753 / % possible obs: 98.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Net I/σ(I): 8.1
Reflection shellResolution: 2.03→2.08 Å / Rmerge(I) obs: 1.051 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1684 / CC1/2: 0.653 / Rpim(I) all: 0.624

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
pointlessdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YAW

6yaw


Resolution: 2.03→41.8 Å / SU ML: 0.3198 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.8723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2546 1419 4.79 %
Rwork0.2175 28230 -
obs0.2192 29649 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.98 Å2
Refinement stepCycle: LAST / Resolution: 2.03→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 58 49 3577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01093595
X-RAY DIFFRACTIONf_angle_d1.28034828
X-RAY DIFFRACTIONf_chiral_restr0.0728530
X-RAY DIFFRACTIONf_plane_restr0.0101612
X-RAY DIFFRACTIONf_dihedral_angle_d20.23811435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.3693950.34612309X-RAY DIFFRACTION80.35
2.1-2.190.30171310.28392889X-RAY DIFFRACTION99.9
2.19-2.290.3131540.26972858X-RAY DIFFRACTION99.34
2.29-2.410.3071510.2642844X-RAY DIFFRACTION99.47
2.41-2.560.29191620.24982864X-RAY DIFFRACTION99.64
2.56-2.760.28221610.24712844X-RAY DIFFRACTION99.9
2.76-3.030.33751500.2412882X-RAY DIFFRACTION99.87
3.03-3.470.24471180.23462917X-RAY DIFFRACTION99.74
3.47-4.380.22381620.18632876X-RAY DIFFRACTION99.8
4.38-41.80.20571350.17672947X-RAY DIFFRACTION99.68

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