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- PDB-1eog: CRYSTAL STRUCTURE OF PI CLASS GLUTATHIONE TRANSFERASE -

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Entry
Database: PDB / ID: 1eog
TitleCRYSTAL STRUCTURE OF PI CLASS GLUTATHIONE TRANSFERASE
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / glutathione transferase / helix capping mutant (S149A)
Function / homology
Function and homology information


S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process ...S-nitrosoglutathione binding / nitric oxide storage / negative regulation of leukocyte proliferation / TRAF2-GSTP1 complex / negative regulation of smooth muscle cell chemotaxis / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / cellular response to cell-matrix adhesion / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / response to L-ascorbic acid / linoleic acid metabolic process / Glutathione conjugation / nitric oxide binding / negative regulation of monocyte chemotactic protein-1 production / JUN kinase binding / glutathione peroxidase activity / oligodendrocyte development / Paracetamol ADME / 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 / Detoxification of Reactive Oxygen Species / negative regulation of acute inflammatory response / glutathione transferase / negative regulation of vascular associated smooth muscle cell proliferation / glutathione transferase activity / protein serine/threonine kinase inhibitor activity / negative regulation of tumor necrosis factor production / animal organ regeneration / negative regulation of tumor necrosis factor-mediated signaling pathway / response to amino acid / toxic substance binding / regulation of ERK1 and ERK2 cascade / negative regulation of fibroblast proliferation / positive regulation of superoxide anion generation / negative regulation of MAPK cascade / negative regulation of canonical NF-kappaB signal transduction / glutathione metabolic process / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / fatty acid binding / central nervous system development / response to reactive oxygen species / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of ERK1 and ERK2 cascade / cellular response to insulin stimulus / response to estradiol / cellular response to lipopolysaccharide / response to ethanol / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-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. ...Glutathione S-transferase, Pi class / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-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
Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRossjohn, J. / McKinstry, W.J. / Oakley, A.J. / Parker, M.W. / Stenberg, G. / Mannervik, B. / Dragani, B. / Cocco, R. / Aceto, A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structures of thermolabile mutants of human glutathione transferase P1-1.
Authors: Rossjohn, J. / McKinstry, W.J. / Oakley, A.J. / Parker, M.W. / Stenberg, G. / Mannervik, B. / Dragani, B. / Cocco, R. / Aceto, A.
History
DepositionMar 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 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
B: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)46,2672
Polymers46,2672
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-14 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.870, 91.010, 69.070
Angle α, β, γ (deg.)90.00, 98.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE


Mass: 23133.455 Da / Num. of mol.: 2 / Mutation: S149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: XL-1 BLUE / Organ (production host): LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P09211, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.0 mg/mlprotein1drop
210 mMHEPES1drop
320-25 %(w/v)ammonium sulfate1reservoir
460 mMdithiothreitol1reservoir
5100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 26251 / Num. obs: 23250
Reflection
*PLUS
% possible obs: 91.6 % / Redundancy: 1.8 % / Num. measured all: 48527 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2

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Processing

SoftwareName: CNS / Classification: refinement
RefinementResolution: 2.1→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2382 2167 7.6 %
Rwork0.2036 --
all0.2036 26093 -
obs0.2036 23250 91.4 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.222 Å20 Å2-0.904 Å2
2--4.203 Å20 Å2
3---4.019 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 0 117 3377
Refinement
*PLUS
Rfactor Rfree: 0.238 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.26
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg21.7
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.76

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