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- PDB-5yvn: Human Glutathione Transferase Omega1 -

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Basic information

Entry
Database: PDB / ID: 5yvn
TitleHuman Glutathione Transferase Omega1
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE / Inhibitor / GST / allosteric
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 / xenobiotic catabolic process / glutathione metabolic 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
ACETATE ION / GLUTATHIONE / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsSaisawang, C. / Ketterman, A. / Wongsantichon, J.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Mahidol University Thailand
CitationJournal: Proteins / Year: 2019
Title: Glutathione transferase Omega 1-1 (GSTO1-1) modulates Akt and MEK1/2 signaling in human neuroblastoma cell SH-SY5Y.
Authors: Saisawang, C. / Wongsantichon, J. / Robinson, R.C. / Ketterman, A.J.
History
DepositionNov 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,2546
Polymers27,6001
Non-polymers6555
Water5,296294
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,50912
Polymers55,2002
Non-polymers1,30910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4710 Å2
ΔGint-110 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.226, 57.226, 140.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glutathione S-transferase omega-1 / Glutathione Transferase / GSTO-1 / Glutathione S-transferase omega 1-1 / GSTO 1-1 / Glutathione- ...Glutathione Transferase / 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: 27599.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTO1, GSTTLP28 / Production host: Escherichia coli (E. coli)
References: UniProt: P78417, glutathione transferase, glutathione dehydrogenase (ascorbate), methylarsonate reductase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2 M Ammonium sulfate, 100 mM Sodium acetate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→20 Å / Num. obs: 60978 / % possible obs: 98.4 % / Redundancy: 6.1 % / Net I/σ(I): 38.88
Reflection shellResolution: 1.33→1.35 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EEM

1eem


Resolution: 1.33→18.732 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.15
RfactorNum. reflection% reflection
Rfree0.1941 2788 4.98 %
Rwork0.1747 --
obs0.1757 55985 90.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.33→18.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 39 294 2254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082015
X-RAY DIFFRACTIONf_angle_d1.0862722
X-RAY DIFFRACTIONf_dihedral_angle_d12.412771
X-RAY DIFFRACTIONf_chiral_restr0.042286
X-RAY DIFFRACTIONf_plane_restr0.006348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3301-1.3530.2458290.2272780X-RAY DIFFRACTION27
1.353-1.37760.2428620.22511299X-RAY DIFFRACTION44
1.3776-1.40410.2642990.22281698X-RAY DIFFRACTION59
1.4041-1.43270.23751410.22672376X-RAY DIFFRACTION81
1.4327-1.46390.23871320.2092848X-RAY DIFFRACTION99
1.4639-1.49790.22471360.19612909X-RAY DIFFRACTION100
1.4979-1.53530.19571640.19352897X-RAY DIFFRACTION100
1.5353-1.57680.19311680.18592928X-RAY DIFFRACTION100
1.5768-1.62320.2161400.17322901X-RAY DIFFRACTION100
1.6232-1.67560.19761740.17892916X-RAY DIFFRACTION100
1.6756-1.73540.20441510.17412926X-RAY DIFFRACTION100
1.7354-1.80480.17951610.17152909X-RAY DIFFRACTION100
1.8048-1.88690.19451510.17872909X-RAY DIFFRACTION100
1.8869-1.98630.19841600.17792939X-RAY DIFFRACTION100
1.9863-2.11060.17911480.17152960X-RAY DIFFRACTION100
2.1106-2.27330.21471370.16972953X-RAY DIFFRACTION100
2.2733-2.50160.21271540.17532947X-RAY DIFFRACTION99
2.5016-2.86250.19951750.17772990X-RAY DIFFRACTION100
2.8625-3.60220.17421500.16792993X-RAY DIFFRACTION99
3.6022-18.73350.17541560.16173119X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56910.01490.13731.0980.08512.4621-0.01030.1060.048-0.1615-0.052-0.0664-0.16760.10660.05440.0901-0.0130.00710.10520.0120.098725.3122-13.10927.3124
21.8320.0511-0.33051.6791-0.00782.1414-0.08090.1716-0.0039-0.1767-0.00230.22390.0669-0.26780.07270.091-0.0171-0.00720.1301-0.00830.098516.1122-17.75185.8308
30.79810.5525-0.67480.4544-0.40881.82890.0133-0.0992-0.0710.0361-0.0373-0.00140.1870.08340.0220.0979-0.00670.00780.10970.0050.110121.1167-24.715925.2196
40.04450.02340.06444.02960.44370.0711-0.07330.10590.3864-0.78090.1430.6569-0.2069-0.0334-0.06870.2381-0.0206-0.0210.15330.03260.324213.99130.350625.0576
50.5934-0.62530.56014.3811-1.86860.9524-0.0663-0.07010.05840.31850.11860.3974-0.1182-0.1565-0.05720.22440.01190.05550.231-0.01560.193817.6621-3.114436.1708
60.77450.2103-0.42520.71140.21111.6010.049-0.16660.04920.1958-0.1233-0.10590.07150.15390.06350.1128-0.0219-0.01680.13020.00920.105426.6698-14.888429.8377
70.54450.3401-0.40661.9145-1.92421.91970.0442-0.13820.19160.40560.04270.0594-0.43750.1811-0.04440.2891-0.0269-0.00240.1979-0.04330.280124.75441.039731.5392
81.20670.1647-0.49870.83990.11342.1452-0.0096-0.09450.13790.09330.0092-0.1082-0.20450.29920.02270.1137-0.024-0.02250.1458-0.00880.145532.2988-9.281328.7885
90.51570.3245-0.20562.12630.9064.74190.2231-0.0280.23420.08890.12670.0248-1.02530.1988-0.23610.4677-0.06830.05790.17490.00320.247224.59793.391811.4447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 135 )
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 182 )
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 196 )
8X-RAY DIFFRACTION8chain 'A' and (resid 197 through 218 )
9X-RAY DIFFRACTION9chain 'A' and (resid 219 through 241 )

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