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- PDB-2vo4: Glutathione transferase from Glycine max -

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Basic information

Entry
Database: PDB / ID: 2vo4
TitleGlutathione transferase from Glycine max
Components2,4-D INDUCIBLE GLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / HERBICIDE / GLYCINE MAX / TAU CLASS GST / S-(P-NITROBENZYL- GLUTATHIONE)
Function / homology
Function and homology information


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 S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione transferase family / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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 S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione transferase family / 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
4-NITROPHENYL METHANETHIOL / S-(P-NITROBENZYL)GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAxarli, I. / Dhavala, P. / Papageorgiou, A.C. / Labrou, N.E.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystallographic and Functional Characterization of the Fluorodifen-Inducible Glutathione Transferase from Glycine Max Reveals an Active Site Topography Suited for Diphenylether Herbicides and a Novel L-Site.
Authors: Axarli, I. / Dhavala, P. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionFeb 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.0Apr 15, 2026Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_contact_author.country / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,4-D INDUCIBLE GLUTATHIONE S-TRANSFERASE
B: 2,4-D INDUCIBLE GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7698
Polymers51,3612
Non-polymers1,4076
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-17 kcal/mol
Surface area24010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)91.375, 91.375, 111.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2104-

HOH

21B-2211-

HOH

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Components

#1: Protein 2,4-D INDUCIBLE GLUTATHIONE S-TRANSFERASE / GLUTATHIONE-S-TRANSFERASE / GSTA


Mass: 25680.699 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GLYCINE MAX (soybean) / References: UniProt: O49235, glutathione transferase
#2: Chemical ChemComp-GTB / S-(P-NITROBENZYL)GLUTATHIONE


Mass: 442.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22N4O8S
#3: Chemical ChemComp-4NM / (4-nitrophenyl)methanethiol


Mass: 169.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7NO2S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growDetails: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8088
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 1.75→70.71 Å / Num. obs: 48045 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 42 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYJ

1oyj


Resolution: 1.75→70.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.379 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2400 5.1 %RANDOM
Rwork0.194 ---
obs0.197 45117 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3622 0 94 430 4146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223909
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9965289
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0645466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22724.783184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98415732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1611519
X-RAY DIFFRACTIONr_chiral_restr0.1280.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022973
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22058
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4540.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9421.52308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48323644
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41131853
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7214.51632
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 174
Rwork0.24 3280
Refinement TLS params.Method: refined / Origin x: 22.6605 Å / Origin y: -23.4754 Å / Origin z: -5.9035 Å
111213212223313233
T-0.0927 Å2-0.0196 Å2-0.0021 Å2-0.0514 Å2-0.0126 Å2---0.0676 Å2
L0.7422 °2-0.1467 °2-0.0801 °2-0.5281 °20.0416 °2--0.4149 °2
S-0.0225 Å °-0.2613 Å °0.0294 Å °0.0288 Å °0.0511 Å °-0.0105 Å °-0.0109 Å °0.0167 Å °-0.0286 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 219
2X-RAY DIFFRACTION1A1 - 219

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