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- PDB-8qll: Crystal structure of rat glutathione transferase Omega 1 bound to... -

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Basic information

Entry
Database: PDB / ID: 8qll
TitleCrystal structure of rat glutathione transferase Omega 1 bound to glutathione
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE / glutathione transferase Omega / thiol-transferase / ligandin
Function / homology
Function and homology information


methylarsonate reductase / methylarsonate reductase activity / Vitamin C (ascorbate) metabolism / Glutathione conjugation / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / Methylation / cellular response to arsenic-containing substance / L-ascorbic acid biosynthetic process ...methylarsonate reductase / methylarsonate reductase activity / Vitamin C (ascorbate) metabolism / Glutathione conjugation / glutathione dehydrogenase (ascorbate) activity / L-ascorbic acid metabolic process / glutathione dehydrogenase (ascorbate) / Methylation / cellular response to arsenic-containing substance / L-ascorbic acid biosynthetic process / glutathione transferase / glutathione transferase activity / basement membrane / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / cell body / nuclear membrane / oxidoreductase activity / axon / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / : / 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, omega-class / Glutathione S-transferase Omega/Tau-like / : / 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 / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchwartz, M. / Neiers, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Rattus norvegicus Glutathione Transferase Omega 1 Localization in Oral Tissues and Interactions with Food Phytochemicals.
Authors: Poirier, N. / Menetrier, F. / Moreno, J. / Boichot, V. / Heydel, J.M. / Didierjean, C. / Canivenc-Lavier, M.C. / Canon, F. / Neiers, F. / Schwartz, M.
History
DepositionSep 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase omega-1
B: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6824
Polymers57,0682
Non-polymers6152
Water48627
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-26 kcal/mol
Surface area21740 Å2
Unit cell
Length a, b, c (Å)133.164, 133.164, 88.514
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 241 or resid 301))
d_2ens_1(chain "B" and (resid 6 through 98 or (resid 99...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALALEULEUAA6 - 24112 - 247
d_12GSHGSHGSHGSHAC301
d_21ALAALALEULEUBB6 - 24112 - 247
d_22GSHGSHGSHGSHBD301

NCS oper: (Code: givenMatrix: (-0.996295468764, -0.085585726858, 0.00839179829645), (-0.0859945103815, 0.990917751446, -0.10337772513), (0.000532075847656, -0.103716407704, -0.99460676836)Vector: 138. ...NCS oper: (Code: given
Matrix: (-0.996295468764, -0.085585726858, 0.00839179829645), (-0.0859945103815, 0.990917751446, -0.10337772513), (0.000532075847656, -0.103716407704, -0.99460676836)
Vector: 138.056755949, 6.35490735873, 7.97716412769)

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Components

#1: Protein Glutathione S-transferase omega-1


Mass: 28533.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gsto1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z339
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 2 M ammonium sulfate, 100 mM Na acetate pH 4.6, 10 mM glutathione

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.4→49.41 Å / Num. obs: 30224 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 52.09 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1 / Num. unique obs: 3048 / CC1/2: 0.896 / Rpim(I) all: 0.272 / Rrim(I) all: 0.711

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.08 Å / SU ML: 0.3897 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.5416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2958 1592 5.28 %
Rwork0.2521 28577 -
obs0.2544 30169 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3797 0 40 27 3864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743939
X-RAY DIFFRACTIONf_angle_d0.97845329
X-RAY DIFFRACTIONf_chiral_restr0.0567567
X-RAY DIFFRACTIONf_plane_restr0.0082687
X-RAY DIFFRACTIONf_dihedral_angle_d15.55481489
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.843813804047 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.45041630.38862468X-RAY DIFFRACTION95.57
2.48-2.570.39711750.36132552X-RAY DIFFRACTION99.71
2.57-2.670.47871330.36212630X-RAY DIFFRACTION99.75
2.67-2.790.36081490.34992568X-RAY DIFFRACTION99.89
2.79-2.940.39171440.33342594X-RAY DIFFRACTION99.74
2.94-3.120.39151180.34662639X-RAY DIFFRACTION99.49
3.12-3.360.41021440.3132611X-RAY DIFFRACTION99.93
3.36-3.70.29421470.25742605X-RAY DIFFRACTION99.89
3.7-4.230.26971230.21542621X-RAY DIFFRACTION99.78
4.24-5.330.22691490.18912628X-RAY DIFFRACTION99.89
5.34-47.080.19931470.18832661X-RAY DIFFRACTION99.01

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