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- PDB-3lfl: Crystal Structure of human Glutathione Transferase Omega 1, delta 155 -

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Basic information

Entry
Database: PDB / ID: 3lfl
TitleCrystal Structure of human Glutathione Transferase Omega 1, delta 155
ComponentsGlutathione S-transferase omega-1
KeywordsTRANSFERASE / Glutathione S-transferase omega 1 del155 / protein-glutathione complex / N-terminal Thioredoxin-like domain / C-terminal alpha-helical domain
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / GLUTATHIONE / Glutathione S-transferase omega-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrock, J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Novel folding and stability defects cause a deficiency of human glutathione transferase omega 1.
Authors: Zhou, H. / Brock, J. / Casarotto, M.G. / Oakley, A.J. / Board, P.G.
History
DepositionJan 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Non-polymer description
Revision 1.3May 9, 2012Group: Data collection
Revision 1.4Nov 1, 2017Group: Advisory / Refinement description / Structure summary
Category: audit_author / pdbx_unobs_or_zero_occ_atoms / software
Item: _audit_author.name
Revision 1.5Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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_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
B: Glutathione S-transferase omega-1
C: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7979
Polymers82,4123
Non-polymers1,3856
Water5,909328
1
A: Glutathione S-transferase omega-1
hetero molecules

A: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8656
Polymers54,9412
Non-polymers9234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3800 Å2
ΔGint-31 kcal/mol
Surface area21570 Å2
MethodPISA
2
B: Glutathione S-transferase omega-1
C: Glutathione S-transferase omega-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8656
Polymers54,9412
Non-polymers9234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-28 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.009, 201.942, 53.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glutathione S-transferase omega-1 / GSTO 1-1


Mass: 27470.732 Da / Num. of mol.: 3
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
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 48.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.2M trimethyl amine N-oxide dihydrate, 20% (w/v) polyethylene glycol monomethyl ether 2000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5406 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 47137 / Num. obs: 44498 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.128 / Χ2: 1.203 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Num. unique all: 3715 / Χ2: 1.139 / % possible all: 80.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.505 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1731 5.1 %RANDOM
Rwork0.199 ---
obs0.202 33943 72.08 %-
all-33951 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.943 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 96.9 Å2 / Biso mean: 31.343 Å2 / Biso min: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.088 Å20 Å20 Å2
2--0.007 Å2-0 Å2
3----2.095 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5547 0 84 328 5959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075768
X-RAY DIFFRACTIONf_angle_d1.0267777
X-RAY DIFFRACTIONf_chiral_restr0.07823
X-RAY DIFFRACTIONf_plane_restr0.011982
X-RAY DIFFRACTIONf_dihedral_angle_d17.6172213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1620.2981650.2363337350290
2.162-2.2320.3151750.2283228340388
2.232-2.3110.2921570.2223150330786
2.311-2.4040.2771550.223014316982
2.404-2.5130.3291670.2252861302878
2.513-2.6460.291450.2152719286474
2.646-2.8110.2881410.2162435257666
2.811-3.0280.2871110.2092198230959
3.028-3.3330.251920.2012052214454
3.333-3.8150.2241060.1821875198150
3.815-4.8050.1961350.1542054218955
4.805-36.510.1941820.1653289347183

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