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- PDB-1eoh: GLUTATHIONE TRANSFERASE P1-1 -

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Basic information

Entry
Database: PDB / ID: 1eoh
TitleGLUTATHIONE TRANSFERASE P1-1
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / glutathione transferase / helix capping mutant (D152A)
Function / homology
Function and homology information


nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process ...nitric oxide storage / S-nitrosoglutathione binding / kinase regulator activity / negative regulation of biosynthetic process / TRAF2-GSTP1 complex / dinitrosyl-iron complex binding / common myeloid progenitor cell proliferation / hepoxilin biosynthetic process / glutathione derivative biosynthetic process / negative regulation of nitric-oxide synthase biosynthetic process / negative regulation of JUN kinase activity / nitric oxide binding / linoleic acid metabolic process / negative regulation of leukocyte proliferation / Glutathione conjugation / negative regulation of monocyte chemotactic protein-1 production / Paracetamol ADME / JUN kinase binding / glutathione peroxidase activity / negative regulation of stress-activated MAPK cascade / negative regulation of interleukin-1 beta production / regulation of stress-activated MAPK cascade / prostaglandin metabolic process / negative regulation of MAPK cascade / Detoxification of Reactive Oxygen Species / glutathione transferase / negative regulation of acute inflammatory response / glutathione transferase activity / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / glutathione metabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of fibroblast proliferation / xenobiotic metabolic process / regulation of ERK1 and ERK2 cascade / response to reactive oxygen species / positive regulation of superoxide anion generation / negative regulation of MAP kinase activity / central nervous system development / fatty acid binding / negative regulation of extrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / negative regulation of ERK1 and ERK2 cascade / secretory granule lumen / cellular response to lipopolysaccharide / vesicle / ficolin-1-rich granule lumen / Neutrophil degranulation / negative regulation of apoptotic process / mitochondrion / extracellular space / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
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, 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, Pi 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
Glutathione S-transferase P
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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 1.3Nov 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 1.4Feb 7, 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
B: GLUTATHIONE S-TRANSFERASE
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE
E: GLUTATHIONE S-TRANSFERASE
F: GLUTATHIONE S-TRANSFERASE
G: GLUTATHIONE S-TRANSFERASE
H: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)185,6208
Polymers185,6208
Non-polymers00
Water9,008500
1
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)46,4052
Polymers46,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-14 kcal/mol
Surface area17760 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)46,4052
Polymers46,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-15 kcal/mol
Surface area17800 Å2
MethodPISA
3
E: GLUTATHIONE S-TRANSFERASE
F: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)46,4052
Polymers46,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-15 kcal/mol
Surface area17720 Å2
MethodPISA
4
G: GLUTATHIONE S-TRANSFERASE
H: GLUTATHIONE S-TRANSFERASE


Theoretical massNumber of molelcules
Total (without water)46,4052
Polymers46,4052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-15 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.970, 84.020, 236.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE /


Mass: 23202.561 Da / Num. of mol.: 8 / Mutation: D152A
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 / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
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

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 57974 / % possible obs: 99 % / Redundancy: 4 % / Num. measured all: 231441 / Rmerge(I) obs: 0.115
Reflection shell
*PLUS
% possible obs: 58 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.4

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Processing

SoftwareName: CNS / Version: 0.4 / Classification: refinement
RefinementResolution: 2.5→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.2864 -
Rwork0.2314 -
all-57589
obs-58096
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13080 0 0 500 13580
Software
*PLUS
Version: 0.4 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 54671 / Num. reflection Rfree: 2918 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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