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- PDB-1gul: HUMAN GLUTATHIONE TRANSFERASE A4-4 COMPLEX WITH IODOBENZYL GLUTATHIONE -

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Basic information

Entry
Database: PDB / ID: 1gul
TitleHUMAN GLUTATHIONE TRANSFERASE A4-4 COMPLEX WITH IODOBENZYL GLUTATHIONE
ComponentsGlutathione S-transferase A4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / OXIDATIVE STRESS / ALKENAL DEGRADATION / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Glutathione conjugation / glutathione transferase / glutathione transferase activity / glutathione metabolic process / xenobiotic metabolic process / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / 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, alpha class / 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
GAMMA-GLUTAMYL[S-(2-IODOBENZYL)CYSTEINYL]GLYCINE / Glutathione S-transferase A4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBruns, C.M. / Hubatsch, I. / Ridderstrom, M. / Mannervik, B. / Tainer, J.A.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products
Authors: Bruns, C.M. / Hubatsch, I. / Ridderstrom, M. / Mannervik, B. / Tainer, J.A.
#1: Journal: Biochem.J. / Year: 1998
Title: Human Glutathione Transferase A4-4: An Alpha Class Enzyme with High Catalytic Efficiency in the Conjugation of 4-Hydroxynonenal and Other Genotoxic Products of Lipid Peroxidation
Authors: Hubatsch, I. / Ridderstrom, M. / Mannervik, B.
History
DepositionJun 10, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.3Jul 21, 2021Group: Advisory / Derived calculations / Refinement description
Category: pdbx_validate_polymer_linkage / refine / struct_conn
Item: _refine.ls_percent_reflns_obs / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jun 7, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.type / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _struct_asym.entity_id / _struct_conf.beg_label_asym_id / _struct_conf.end_label_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.end_label_asym_id / _struct_site_gen.label_asym_id
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase A4
B: Glutathione S-transferase A4
C: Glutathione S-transferase A4
D: Glutathione S-transferase A4
E: Glutathione S-transferase A4
F: Glutathione S-transferase A4
G: Glutathione S-transferase A4
H: Glutathione S-transferase A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,09116
Polymers205,9058
Non-polymers4,1878
Water3,891216
1
A: Glutathione S-transferase A4
B: Glutathione S-transferase A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5234
Polymers51,4762
Non-polymers1,0472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-17 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: Glutathione S-transferase A4
D: Glutathione S-transferase A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5234
Polymers51,4762
Non-polymers1,0472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-17 kcal/mol
Surface area18490 Å2
MethodPISA
3
E: Glutathione S-transferase A4
F: Glutathione S-transferase A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5234
Polymers51,4762
Non-polymers1,0472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-17 kcal/mol
Surface area18440 Å2
MethodPISA
4
G: Glutathione S-transferase A4
H: Glutathione S-transferase A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5234
Polymers51,4762
Non-polymers1,0472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-17 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.300, 156.100, 101.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Glutathione S-transferase A4 / E.C.2.5.1.18 / GST class-alpha member 4 / Glutathione S-transferase A4-4


Mass: 25738.094 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: SUBSTANTIA NIGRA / Gene: GSTA4 / Organ: BRAIN / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O15217, glutathione transferase
#2: Chemical
ChemComp-IBG / GAMMA-GLUTAMYL[S-(2-IODOBENZYL)CYSTEINYL]GLYCINE


Mass: 523.343 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H22IN3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3 Å3/Da / Density % sol: 55 %
Crystal growpH: 7
Details: CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 100 MM PH 7.0, THEN SOAKED IN 1MM IODOBENZYL GLUTATHIONE
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(w/v)PEG60001reservoir
2100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→160 Å / Num. obs: 75834 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rsym value: 0.11 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.41 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. obs: 58800 / Rmerge(I) obs: 0.11

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSE

1gse


Resolution: 2.7→160 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3294 5 %RANDOM
Rwork0.248 ---
obs0.25 58800 86 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 565.9 Å2 / ksol: 1.02 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→160 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14440 0 0 216 14656
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01918470.8
X-RAY DIFFRACTIONt_angle_deg2.7724781.5
X-RAY DIFFRACTIONt_dihedral_angle_d15.510950.5
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.021501
X-RAY DIFFRACTIONt_gen_planes0.0162564
X-RAY DIFFRACTIONt_it5.9718352
X-RAY DIFFRACTIONt_nbd0.036310
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d0.8
X-RAY DIFFRACTIONt_angle_deg1.52.77
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_planar_d10.021
X-RAY DIFFRACTIONt_plane_restr40.016
X-RAY DIFFRACTIONt_dihedral_angle_deg0.515.5

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