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- PDB-1gsy: GLUTATHIONE S-TRANSFERASE YFYF, CLASS PI, COMPLEXED WITH GLUTATHIONE -

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Basic information

Entry
Database: PDB / ID: 1gsy
TitleGLUTATHIONE S-TRANSFERASE YFYF, CLASS PI, COMPLEXED WITH GLUTATHIONE
ComponentsGLUTATHIONE S-TRANSFERASE CLASS PI
KeywordsTRANSFERASE / MULTIGENE FAMILY
Function / homology
Function and homology information


negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / negative regulation of leukocyte proliferation / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid ...negative regulation of neutrophil aggregation / Paracetamol ADME / Glutathione conjugation / Detoxification of Reactive Oxygen Species / negative regulation of leukocyte proliferation / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / oligodendrocyte development / negative regulation of stress-activated MAPK cascade / negative regulation of JNK cascade / prostaglandin metabolic process / negative regulation of interleukin-1 beta production / cellular response to glucocorticoid stimulus / regulation of stress-activated MAPK cascade / negative regulation of acute inflammatory response / glutathione transferase / glutathione transferase activity / protein serine/threonine kinase inhibitor activity / negative regulation of tumor necrosis factor production / animal organ regeneration / response to amino acid / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / positive regulation of superoxide anion generation / Neutrophil degranulation / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / response to nutrient levels / negative regulation of ERK1 and ERK2 cascade / response to toxic substance / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / inflammatory response / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleus / cytosol
Similarity search - Function
Glutathione S-transferase, Pi class / 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, Pi class / 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
GLUTATHIONE / Glutathione S-transferase P 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsParraga, A. / Garcia-Saez, I. / Coll, M.
CitationJournal: Biochem.J. / Year: 1998
Title: The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism.
Authors: Parraga, A. / Garcia-Saez, I. / Walsh, S.B. / Mantle, T.J. / Coll, M.
History
DepositionOct 25, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 14, 2011Group: Non-polymer description
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE CLASS PI
B: GLUTATHIONE S-TRANSFERASE CLASS PI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6234
Polymers47,0082
Non-polymers6152
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-15 kcal/mol
Surface area18160 Å2
MethodPISA
2
A: GLUTATHIONE S-TRANSFERASE CLASS PI
B: GLUTATHIONE S-TRANSFERASE CLASS PI
hetero molecules

A: GLUTATHIONE S-TRANSFERASE CLASS PI
B: GLUTATHIONE S-TRANSFERASE CLASS PI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2458
Polymers94,0164
Non-polymers1,2294
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area8690 Å2
ΔGint-43 kcal/mol
Surface area35090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.680, 162.570, 63.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE CLASS PI / GST YFYF


Mass: 23503.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GLUTATHIONE COMMERCIALLY PROVIDED BY SIGMA / Source: (natural) Mus musculus (house mouse) / Organ: LIVER / References: UniProt: P19157, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.9 Å3/Da / Density % sol: 68.5 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.8 mMprotein1drop
250 mMMES1drop
38 %PEG60001drop
40.3 Msodium potassium phospahte1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 20740
Reflection
*PLUS
% possible obs: 82.1 % / Num. measured all: 171889 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.44 Å / Lowest resolution: 2.5 Å / % possible obs: 50.3 % / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GLP

1glp


Resolution: 2.44→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 15756
Refinement stepCycle: LAST / Resolution: 2.44→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 40 131 3479
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_deg1.594
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 / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208 / Rfactor Rfree: 0.287
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.02

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