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- PDB-1gwc: The structure of a tau class glutathione S-transferase from wheat... -

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Basic information

Entry
Database: PDB / ID: 1gwc
TitleThe structure of a tau class glutathione S-transferase from wheat, active in herbicide detoxification
ComponentsGLUTATHIONE S-TRANSFERASE TSI-1
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE / HERBICIDE DETOXIFICATION / PLANT / TAU CLASS
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 ...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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-HEXYLGLUTATHIONE / Glutathione S-transferase 1
Similarity search - Component
Biological speciesAEGILOPS TAUSCHII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsThom, R. / Cummins, I. / Dixon, D.P. / Edwards, R. / Cole, D.J. / Lapthorn, A.J.
Citation
Journal: Biochemistry / Year: 2002
Title: Structure of a Tau Class Glutathione S-Transferase from Wheat Active in Herbicide Detoxification
Authors: Thom, R. / Cummins, I. / Dixon, D.P. / Edwards, R. / Cole, D.J. / Lapthorn, A.J.
#1: Journal: Plant Physiol. / Year: 1997
Title: Partial Characterization of Glutathione S-Transferases from Wheat (Triticum Spp.) And
Authors: Riechers, D.E. / Irzyk, G.P. / Jones, S.S. / Fuerst, E.P.
History
DepositionMar 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2002Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE TSI-1
B: GLUTATHIONE S-TRANSFERASE TSI-1
C: GLUTATHIONE S-TRANSFERASE TSI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0459
Polymers74,5793
Non-polymers1,4666
Water12,809711
1
A: GLUTATHIONE S-TRANSFERASE TSI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3483
Polymers24,8601
Non-polymers4892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUTATHIONE S-TRANSFERASE TSI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3483
Polymers24,8601
Non-polymers4892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: GLUTATHIONE S-TRANSFERASE TSI-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3483
Polymers24,8601
Non-polymers4892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.982, 152.389, 146.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2104-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 4 - 224 / Label seq-ID: 4 - 224

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

NCS oper:
IDCodeMatrixVector
1given(0.50012, -0.86595, -0.00012), (0.86595, 0.50012, 6.0E-5), (1.0E-5, -0.00014, 1)43.99229, -76.18657, 24.45922
2given(0.50121, -0.86533, -0.0005), (-0.86533, -0.50121, 8.0E-5), (-0.00032, 0.00039, -1)43.91304, 76.18964, 122.32704

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE TSI-1 / TAGSTU4-4 GLUTATHIONE S-TRANSFERASE


Mass: 24859.732 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEGILOPS TAUSCHII (plant) / Tissue: SHOOTS
Description: WHEAT SEEDLINGS TREATED FOR 7 DAYS WITH THE WHEAT SAFENER FENCHLORAZOLE-ETHYL
Plasmid: PET11D / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): pLysS / References: UniProt: O04941, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Compound detailsWHEAT SEEDLINGS TREATED FOR 7 DAYS WITH THE WHEAT SAFENER FENCHLORAZOLE-ETHYL

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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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: SITTING DROP METHOD WITH 1 MICROLITRE PROTEIN (10 MG/ML) AND 1 MICROLITRE WELL SOLUTION (1.1-1.5 M AMMONIUM SULPHATE, 0.2M LITHIUM SULPHATE 0.1M TRIS HCL PH 7.5 WITH 5MM S-HEXYLGLUTATHIONE)
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31.1-1.5 Mammonium sulfate1reservoir
40.2 Mlithium sulfate1reservoir
50.1 MTris-HCl1reservoirpH7.5
65 mMS-hexylglutathione1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 1999 / Details: ELLIPSOIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 2.25→53 Å / Num. obs: 44559 / % possible obs: 95.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 11
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 80
Reflection
*PLUS
Lowest resolution: 53 Å

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EEM

1eem


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.362 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2178 5.1 %RANDOM
Rwork0.157 ---
obs0.159 2150 90 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5071 0 93 711 5875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225310
X-RAY DIFFRACTIONr_bond_other_d0.0010.025011
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.351.9937183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.415311659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025810
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021044
X-RAY DIFFRACTIONr_nbd_refined0.2480.31347
X-RAY DIFFRACTIONr_nbd_other0.2180.35096
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0980.53
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.5567
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.21708
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3770.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.357
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.541
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3071.53290
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42725236
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.79232020
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2824.51947
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1282tight positional0.050.05
2B1282tight positional0.050.05
3C1282tight positional0.050.05
1A2004medium positional0.320.5
2B2004medium positional0.280.5
3C2004medium positional0.390.5
1A1282tight thermal0.340.5
2B1282tight thermal0.330.5
3C1282tight thermal0.310.5
1A2004medium thermal0.812
2B2004medium thermal0.842
3C2004medium thermal0.842
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 125
Rwork0.171 2150
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78930.0457-0.1081.3679-0.26110.82780.02890.03230.0524-0.0689-0.00370.0583-0.01230.1-0.02530.08-0.0028-0.00030.0001-0.00150.054849.661-5.49461.289
20.91960.2799-0.21020.3735-0.18270.5094-0.02150.09590.0663-0.03780.04960.05890.0419-0.0861-0.02810.0569-0.0099-0.00730.0094-0.00530.06226430.30836.898
31.07210.1886-0.22140.5484-0.10080.37780.031-0.05340.14490.0062-0.01570.0216-0.09620.132-0.01520.1046-0.0234-0.0040.035-0.00820.074573.66336.03160.976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 224
2X-RAY DIFFRACTION1A1225
3X-RAY DIFFRACTION1B1226
4X-RAY DIFFRACTION2B4 - 224
5X-RAY DIFFRACTION2B1225
6X-RAY DIFFRACTION2A1226
7X-RAY DIFFRACTION3C4 - 225
8X-RAY DIFFRACTION3C1226
9X-RAY DIFFRACTION3C1227
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 40929 / Rfactor obs: 0.157 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.025
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.26
LS refinement shell
*PLUS
Rfactor obs: 0.171

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