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- PDB-4is0: Structural Insights into Omega-Class Glutathione Transferases: A ... -

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Basic information

Entry
Database: PDB / ID: 4is0
TitleStructural Insights into Omega-Class Glutathione Transferases: A Snapshot of Enzyme Reduction and Identification of the Non-Catalytic Ligandin Site.
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE / OXIDOREDUCTASE / GST fold / ligand-binding / Cytosol
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
Chem-1R4 / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / OXIDIZED GLUTATHIONE DISULFIDE / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.721 Å
AuthorsBrock, J. / Oakley, A.J.
CitationJournal: Plos One / Year: 2013
Title: Structural insights into omega-class glutathione transferases: a snapshot of enzyme reduction and identification of a non-catalytic ligandin site.
Authors: Brock, J. / Board, P.G. / Oakley, A.J.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9976
Polymers27,5681
Non-polymers1,4295
Water2,522140
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,99412
Polymers55,1362
Non-polymers2,85910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area6080 Å2
ΔGint-91 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 57.600, 140.176
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1134-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutathione S-transferase omega-1 / GSTO-1 / Glutathione S-transferase omega 1-1 / GSTO 1-1 / Glutathione-dependent dehydroascorbate ...GSTO-1 / Glutathione S-transferase omega 1-1 / GSTO 1-1 / Glutathione-dependent dehydroascorbate reductase / Monomethylarsonic acid reductase / MMA(V) reductase / S-(Phenacyl)glutathione reductase / SPG-R


Mass: 27567.779 Da / Num. of mol.: 1 / Mutation: C32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase

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Non-polymers , 5 types, 145 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 612.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N6O12S2
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-1R4 / L-gamma-glutamyl-S-[2-(4-nitrophenyl)-2-oxoethyl]-L-cysteinylglycine / S-(4-nitrophenacyl)glutathione


Mass: 470.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N4O9S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4349.49
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop4.252.2 M ammonium sulfate, 100 mM sodium acetate pH 4.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2772vapor diffusion, hanging drop4.752.2 M ammonium sulfate, 100 mM sodium acetate pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL4-2 / Wavelength: 1.034375 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: Beamline Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.034375 Å / Relative weight: 1
ReflectionResolution: 1.72→40.64 Å / Num. all: 29422 / Num. obs: 29422 / % possible obs: 99.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 16.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.62
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EEM

1eem


Resolution: 1.721→40.641 Å / SU ML: 0.19 / σ(F): 1.75 / Phase error: 18.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 1997 6.8 %
Rwork0.1519 --
obs0.1552 29370 99.85 %
all-29370 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.721→40.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 90 140 2151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112092
X-RAY DIFFRACTIONf_angle_d1.4242824
X-RAY DIFFRACTIONf_dihedral_angle_d13.857804
X-RAY DIFFRACTIONf_chiral_restr0.067294
X-RAY DIFFRACTIONf_plane_restr0.007364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7213-1.76430.24111390.16681879X-RAY DIFFRACTION98
1.7643-1.8120.29681410.17451933X-RAY DIFFRACTION100
1.812-1.86530.25751380.16141932X-RAY DIFFRACTION100
1.8653-1.92550.22811440.1481917X-RAY DIFFRACTION100
1.9255-1.99440.21461400.14171939X-RAY DIFFRACTION100
1.9944-2.07420.23081470.13151915X-RAY DIFFRACTION100
2.0742-2.16860.21581350.12761935X-RAY DIFFRACTION100
2.1686-2.28290.21931400.12361944X-RAY DIFFRACTION100
2.2829-2.42590.18351400.1281947X-RAY DIFFRACTION100
2.4259-2.61320.20011450.14061976X-RAY DIFFRACTION100
2.6132-2.87610.20831440.15081960X-RAY DIFFRACTION100
2.8761-3.29220.20691410.16711969X-RAY DIFFRACTION100
3.2922-4.14710.17191460.14522016X-RAY DIFFRACTION100
4.1471-40.65220.19241570.17062111X-RAY DIFFRACTION100

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