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- PDB-1eem: GLUTATHIONE TRANSFERASE FROM HOMO SAPIENS -

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Basic information

Entry
Database: PDB / ID: 1eem
TitleGLUTATHIONE TRANSFERASE FROM HOMO SAPIENS
ComponentsGLUTATHIONE-S-TRANSFERASEGlutathione S-transferase
KeywordsTRANSFERASE / GST / Glutathione conjugating / putative oxidoreductase
Function / homology
Function and homology information


positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation ...positive regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / methylarsonate reductase / methylarsonate reductase activity / glutathione dehydrogenase (ascorbate) / glutathione dehydrogenase (ascorbate) activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / Methylation / cellular response to arsenic-containing substance / Glutathione conjugation / positive regulation of ryanodine-sensitive calcium-release channel activity / glutathione transferase / glutathione transferase activity / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / glutathione metabolic process / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / oxidoreductase activity / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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 ...Glutathione S-transferase, omega-class / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / 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 / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBoard, P. / Coggan, M. / Chelvanayagam, G. / Easteal, S. / Jermiin, L.S. / Schulte, G.K. / Danley, D.E. / Hoth, L.R. / Griffor, M.C. / Kamath, A.V. ...Board, P. / Coggan, M. / Chelvanayagam, G. / Easteal, S. / Jermiin, L.S. / Schulte, G.K. / Danley, D.E. / Hoth, L.R. / Griffor, M.C. / Kamath, A.V. / Rosner, M.H. / Chrunyk, B.A. / Perregaux, D.E. / Gabel, C.A. / Geoghegan, K.F. / Pandit, J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Identification, characterization, and crystal structure of the Omega class glutathione transferases.
Authors: Board, P.G. / Coggan, M. / Chelvanayagam, G. / Easteal, S. / Jermiin, L.S. / Schulte, G.K. / Danley, D.E. / Hoth, L.R. / Griffor, M.C. / Kamath, A.V. / Rosner, M.H. / Chrunyk, B.A. / ...Authors: Board, P.G. / Coggan, M. / Chelvanayagam, G. / Easteal, S. / Jermiin, L.S. / Schulte, G.K. / Danley, D.E. / Hoth, L.R. / Griffor, M.C. / Kamath, A.V. / Rosner, M.H. / Chrunyk, B.A. / Perregaux, D.E. / Gabel, C.A. / Geoghegan, K.F. / Pandit, J.
History
DepositionFeb 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE-S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0994
Polymers27,6001
Non-polymers4993
Water1,982110
1
A: GLUTATHIONE-S-TRANSFERASE
hetero molecules

A: GLUTATHIONE-S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1998
Polymers55,2002
Non-polymers9996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)57.090, 57.090, 140.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer constructed from chain A and a symmetry partner generated by the two-fold.

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Components

#1: Protein GLUTATHIONE-S-TRANSFERASE / Glutathione S-transferase


Mass: 27599.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P78417
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 50mM sodium acetate, 1.0M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMdithiothreitol1drop
22 mMGSH-GSSG1drop
38-12 mg/mlprotein1drop
450 mMsodium acetate1drop
51.0-1.2 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 17106 / Num. obs: 17105 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 23.48 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 17.13
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.394 / Num. unique all: 1432 / % possible all: 78.2
Reflection shell
*PLUS
% possible obs: 78.2 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 879 -random
Rwork0.219 ---
all-17105 --
obs-17105 92 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 30 110 2053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.21

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