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- PDB-1bay: GLUTATHIONE S-TRANSFERASE YFYF CYS 47-CARBOXYMETHYLATED CLASS PI,... -

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Basic information

Entry
Database: PDB / ID: 1bay
TitleGLUTATHIONE S-TRANSFERASE YFYF CYS 47-CARBOXYMETHYLATED CLASS PI, FREE ENZYME
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 / cellular response to glucocorticoid stimulus / negative regulation of interleukin-1 beta production / 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 S-transferase P 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REEMPLACEMENT / Resolution: 2 Å
AuthorsVega, M.C. / Coll, M.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: The three-dimensional structure of Cys-47-modified mouse liver glutathione S-transferase P1-1. Carboxymethylation dramatically decreases the affinity for glutathione and is associated with a ...Title: The three-dimensional structure of Cys-47-modified mouse liver glutathione S-transferase P1-1. Carboxymethylation dramatically decreases the affinity for glutathione and is associated with a loss of electron density in the alphaB-310B region.
Authors: Vega, M.C. / Walsh, S.B. / Mantle, T.J. / Coll, M.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Molecular Structure at 1.8 A of Mouse Liver Class Pi Glutathione S-Transferase Complexed with S-(P-Nitrobenzyl)Glutathione and Other Inhibitors
Authors: Garcia-Saez, I. / Parraga, A. / Phillips, M.F. / Mantle, T.J. / Coll, M.
History
DepositionNov 2, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,0082
Polymers47,0082
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.500, 132.500, 63.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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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: CHEMICAL MODIFICATION ON CYS 47 WITH IODOACETIC ACID, CYS 47 CARBOXYMETHYLATED
Source: (natural) Mus musculus (house mouse) / Organ: LIVER / References: UniProt: P19157, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.95 Å3/Da / Density % sol: 60.9 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.5 mg/mlprotein1drop
217 mMHEPES1drop
332 mM1dropCaCl2
44.2 %PEG40001drop
519 %PEG40001reservoir
60.15 M1reservoirCaCl2
775 mMHEPES1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.937
DetectorDetector: IMAGE PLATE / Date: Jul 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28194 / % possible obs: 75 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2→2.5 Å / % possible all: 56.6
Reflection
*PLUS
Num. obs: 31316 / % possible obs: 78.7 % / Observed criterion σ(I): 3
Reflection shell
*PLUS
Lowest resolution: 2.2 Å / % possible obs: 56.8 %

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Processing

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

1glq


Resolution: 2→8 Å / Data cutoff high absF: 50 / Data cutoff low absF: 2 / Cross valid method: BRUNGER'S METHOD / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.236 -10 %RANDOM
Rwork0.193 ---
obs0.193 26183 75 %-
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 0 150 3214
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.337
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: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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