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- PDB-1axd: STRUCTURE OF GLUTATHIONE S-TRANSFERASE-I BOUND WITH THE LIGAND LA... -

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Basic information

Entry
Database: PDB / ID: 1axd
TitleSTRUCTURE OF GLUTATHIONE S-TRANSFERASE-I BOUND WITH THE LIGAND LACTOYLGLUTATHIONE
Components
  • GLUTATHIONE S-TRANSFERASE I
  • LACTOYLGLUTATHIONE
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / HERBICIDE DETOXIFICATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


response to salicylic acid / glutathione binding / response to herbicide / glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to reactive oxygen species / response to hydrogen peroxide / response to xenobiotic stimulus / protein-containing complex / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
Glutathione S-transferase 1
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsNeuefeind, T. / Huber, R. / Dasenbrock, H. / Prade, L. / Bieseler, B.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of herbicide-detoxifying maize glutathione S-transferase-I in complex with lactoylglutathione: evidence for an induced-fit mechanism.
Authors: Neuefeind, T. / Huber, R. / Dasenbrock, H. / Prade, L. / Bieseler, B.
History
DepositionOct 15, 1997Processing site: BNL
Revision 1.0Oct 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_polymer_linkage / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE I
B: GLUTATHIONE S-TRANSFERASE I
C: LACTOYLGLUTATHIONE
D: LACTOYLGLUTATHIONE


Theoretical massNumber of molelcules
Total (without water)47,4214
Polymers47,4214
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.540, 78.910, 55.610
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE I /


Mass: 23330.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Variant: MUTIN / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P12653, glutathione transferase
#2: Protein/peptide LACTOYLGLUTATHIONE


Mass: 379.387 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 %PEG1drop
20.3 Mmagnesium acetate1drop
30.1 MMES1drop
45 mMlactoylglutathione1drop

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 13788 / % possible obs: 92 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Highest resolution: 2.5 Å

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Processing

Software
NameClassification
X-PLORrefinement
CCP4data reduction
RefinementResolution: 2.5→8 Å /
RfactorNum. reflection
Rwork0.174 -
obs0.174 13788
Displacement parametersBiso mean: 31.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 0 190 3518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.4
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6

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