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- PDB-1gnw: STRUCTURE OF GLUTATHIONE S-TRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1gnw
TitleSTRUCTURE OF GLUTATHIONE S-TRANSFERASE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / HERBICIDE DETOXIFICATION
Function / homology
Function and homology information


response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / glutathione binding / apoplast / auxin-activated signaling pathway / plant-type vacuole / plasmodesma ...response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / glutathione binding / apoplast / auxin-activated signaling pathway / plant-type vacuole / plasmodesma / chloroplast stroma / response to zinc ion / glutathione transferase / glutathione transferase activity / response to cadmium ion / response to cold / chloroplast / peroxidase activity / defense response / protein domain specific binding / intracellular membrane-bounded organelle / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / 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 / 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-transferases Phi, C-terminal / 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 / 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 / Glutathione S-transferase F2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsReinemer, P. / Prade, L. / Hof, P. / Neuefeind, T. / Huber, R. / Palme, K. / Bartunik, H.D. / Bieseler, B.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Three-dimensional structure of glutathione S-transferase from Arabidopsis thaliana at 2.2 A resolution: structural characterization of herbicide-conjugating plant glutathione S-transferases ...Title: Three-dimensional structure of glutathione S-transferase from Arabidopsis thaliana at 2.2 A resolution: structural characterization of herbicide-conjugating plant glutathione S-transferases and a novel active site architecture.
Authors: Reinemer, P. / Prade, L. / Hof, P. / Neuefeind, T. / Huber, R. / Zettl, R. / Palme, K. / Schell, J. / Koelln, I. / Bartunik, H.D. / Bieseler, B.
History
DepositionSep 15, 1996Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6336
Polymers48,0632
Non-polymers1,5704
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-56 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.300, 113.300, 69.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 24031.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P46422, glutathione transferase
#2: Chemical
ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
26.7 mMHepes-NaOH1drop
30.02 %1dropNaN3
40.93 Mammonium sulfate1drop
50.067 %PEG40001drop
65.0 mMS-heylglutathione1drop
72.8 Mammonium sulfate1reservoir
80.2 %(w/v)PEG40001reservoir
90.2 MHepes-NaOH1reservoir
100.02 %1reservoirNaN3

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 23438 / % possible obs: 88.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.094
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 9999 Å
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.23 Å / % possible obs: 46.2 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 2.2→8 Å /
RfactorNum. reflection
Rwork0.175 -
obs0.175 21738
Displacement parametersBiso mean: 19.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 26 220 3736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.767
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.7
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg23.028
X-RAY DIFFRACTIONx_improper_angle_deg1.029
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.22 Å / Rfactor obs: 0.289

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