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- PDB-5kej: Crystallographic structure of the Tau class glutathione S-transfe... -

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Basic information

Entry
Database: PDB / ID: 5kej
TitleCrystallographic structure of the Tau class glutathione S-transferase MiGSTU in complex with S-hexyl-glutathione
ComponentsTau class glutathione S-transferase
KeywordsTRANSFERASE / detoxification
Function / homology
Function and homology information


toxin catabolic process / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione transferase family / 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-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione transferase family / 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
S-HEXYLGLUTATHIONE / DI(HYDROXYETHYL)ETHER / glutathione transferase
Similarity search - Component
Biological speciesMangifera indica (mango)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsValenzuela-Chavira, I. / Serrano-Posada, H. / Lopez-Zavala, A. / Hernandez-Paredes, J. / Sotelo-Mundo, R.
CitationJournal: Biochimie / Year: 2017
Title: Insights into ligand binding to a glutathione S-transferase from mango: Structure, thermodynamics and kinetics.
Authors: Valenzuela-Chavira, I. / Contreras-Vergara, C.A. / Arvizu-Flores, A.A. / Serrano-Posada, H. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Hernandez-Paredes, J. / Rudino-Pinera, E. / ...Authors: Valenzuela-Chavira, I. / Contreras-Vergara, C.A. / Arvizu-Flores, A.A. / Serrano-Posada, H. / Lopez-Zavala, A.A. / Garcia-Orozco, K.D. / Hernandez-Paredes, J. / Rudino-Pinera, E. / Stojanoff, V. / Sotelo-Mundo, R.R. / Islas-Osuna, M.A.
History
DepositionJun 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tau class glutathione S-transferase
B: Tau class glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,52310
Polymers51,1012
Non-polymers1,4228
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-14 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.319, 88.805, 96.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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 Tau class glutathione S-transferase


Mass: 25550.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mangifera indica (mango) / Plasmid: pJExpress404 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3
References: UniProt: A0A1P8NWC2*PLUS, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 6
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 6.0, 25%(w/v) polyethylene glycol 3350, 5 mM S-hexyl-glutathione

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 2.35→40.343 Å / Num. obs: 23652 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.8
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on the structure of wheat Tau class glutathione S-transferase (PDB entry 1GWC).

1gwc


Resolution: 2.35→40.343 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.44
RfactorNum. reflection% reflection
Rfree0.2261 1160 4.9 %
Rwork0.1875 --
obs0.1895 23652 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.69 Å2 / Biso mean: 43.4792 Å2 / Biso min: 21.14 Å2
Refinement stepCycle: final / Resolution: 2.35→40.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 94 124 3720
Biso mean--44.37 45.55 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013680
X-RAY DIFFRACTIONf_angle_d1.2194960
X-RAY DIFFRACTIONf_chiral_restr0.044542
X-RAY DIFFRACTIONf_plane_restr0.006614
X-RAY DIFFRACTIONf_dihedral_angle_d15.4521358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3501-2.45710.28441370.223627532890
2.4571-2.58660.28851360.213227802916
2.5866-2.74860.27591230.219927902913
2.7486-2.96080.27741480.205427872935
2.9608-3.25860.21851440.205727852929
3.2586-3.72980.23931580.184328062964
3.7298-4.69810.19371680.1628142982
4.6981-40.34920.20051460.177429773123

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