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- PDB-7bic: Crystal structure of human GSTA1-1 bound to allyl-isothiocyanate -

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Basic information

Entry
Database: PDB / ID: 7bic
TitleCrystal structure of human GSTA1-1 bound to allyl-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 / 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
N-prop-2-en-1-ylthioformamide / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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

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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)102,7825
Polymers102,6804
Non-polymers1011
Water64936
1
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4413
Polymers51,3402
Non-polymers1011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area19150 Å2
MethodPISA
2
C: Glutathione S-transferase A1
D: Glutathione S-transferase A1


Theoretical massNumber of molelcules
Total (without water)51,3402
Polymers51,3402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-22 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.110, 94.650, 104.510
Angle α, β, γ (deg.)90.000, 92.010, 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
Components on special symmetry positions
IDModelComponents
11D-301-

HOH

21D-306-

HOH

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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.: 4
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-9AI / N-prop-2-en-1-ylthioformamide


Mass: 101.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.46→47.33 Å / Num. obs: 35305 / % possible obs: 99 % / Redundancy: 7.09 % / Biso Wilson estimate: 45.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.11
Reflection shellResolution: 2.46→2.6 Å / Rmerge(I) obs: 1.3 / Num. unique obs: 5550 / CC1/2: 0.88 / % possible all: 97.5

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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: 2.46→47.33 Å / SU ML: 0.4115 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.8986
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2769 1761 5.01 %
Rwork0.23 33370 -
obs0.2324 35131 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.38 Å2
Refinement stepCycle: LAST / Resolution: 2.46→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6633 0 6 36 6675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01066768
X-RAY DIFFRACTIONf_angle_d1.30719099
X-RAY DIFFRACTIONf_chiral_restr0.17951008
X-RAY DIFFRACTIONf_plane_restr0.011147
X-RAY DIFFRACTIONf_dihedral_angle_d18.84622652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.520.36171290.34122454X-RAY DIFFRACTION95.1
2.52-2.60.38391330.31442508X-RAY DIFFRACTION97.89
2.6-2.680.37781340.29332564X-RAY DIFFRACTION98.18
2.68-2.780.31631360.28152561X-RAY DIFFRACTION98.39
2.78-2.890.34731360.29052577X-RAY DIFFRACTION98.76
2.89-3.020.3881350.30622557X-RAY DIFFRACTION98.86
3.02-3.180.31361340.28442557X-RAY DIFFRACTION99.15
3.18-3.380.3411360.24612570X-RAY DIFFRACTION98.76
3.38-3.640.2631370.23232608X-RAY DIFFRACTION99.2
3.64-40.26771350.19912559X-RAY DIFFRACTION99.19
4-4.580.22081380.18352618X-RAY DIFFRACTION99.57
4.58-5.770.19341370.18542601X-RAY DIFFRACTION99.49
5.77-47.330.24411410.19642636X-RAY DIFFRACTION98.76

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