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- PDB-1e6b: Crystal structure of a Zeta class glutathione S-transferase from ... -

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Basic information

Entry
Database: PDB / ID: 1e6b
TitleCrystal structure of a Zeta class glutathione S-transferase from Arabidopsis thaliana
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


Isomerases; cis-trans-Isomerases / homogentisate catabolic process / maleylacetoacetate isomerase activity / aromatic amino acid metabolic process / toxin catabolic process / glutathione transferase / glutathione transferase activity / peroxidase activity / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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 ...Glutathione S-transferases, class Zeta , C-terminal / Glutathione S-transferases, class Zeta , N-terminal / Glutathione S-transferases, class Zeta / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / 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
BETA-MERCAPTOETHANOL / Glutathione S-transferase Z1
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.65 Å
AuthorsThom, R. / Lapthorn, A.J.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The Structure of a Zeta Class Glutathione S-Transferase from Arabidopsis Thaliana: Characterisation of a Gst with Novel Active-Site Architecture and a Putative Role in Tyrosine Catabolism.
Authors: Thom, R. / Dixon, D.P. / Edwards, R. / Cole, D.J. / Lapthorn, A.J.
#1: Journal: Arch.Biochem.Biophys. / Year: 2000
Title: Characterisation of a Zeta Class Glutathione Transferase from Arabidopsis Thaliana with a Putative Role in Tyrosine Catabolism
Authors: Dixon, D.P. / Cole, D.J. / Edwards, R.
History
DepositionAug 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9932
Polymers24,9151
Non-polymers781
Water2,450136
1
A: GLUTATHIONE S-TRANSFERASE
hetero molecules

A: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9854
Polymers49,8292
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
MethodPQS
Unit cell
Length a, b, c (Å)75.164, 75.164, 140.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 24914.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET-24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ZVQ3, glutathione transferase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 7.5
Details: 11% PEG 8000, 0.2M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLA, pH 7.50
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMTris-HCl1drop
311 %(w/v)PEG80001reservoir
40.2 Mmagnesium acetate1reservoir
50.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 150341 / % possible obs: 94.7 % / Redundancy: 5 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.65→1.69 Å / % possible all: 95.9
Reflection
*PLUS
Redundancy: 5-6 / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.65→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 -5 %RANDOM
Rwork0.196 ---
obs-150341 94.7 %-
Refinement stepCycle: LAST / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 4 136 1665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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