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- PDB-1ev4: RAT GLUTATHIONE S-TRANSFERASE A1-1: MUTANT W21F/F220Y WITH GSO3 BOUND -

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Basic information

Entry
Database: PDB / ID: 1ev4
TitleRAT GLUTATHIONE S-TRANSFERASE A1-1: MUTANT W21F/F220Y WITH GSO3 BOUND
ComponentsGLUTATHIONE S-TRANSFERASE A1-1
KeywordsTRANSFERASE / disordered C-terminal helices
Function / homology
Function and homology information


Azathioprine ADME / Glutathione conjugation / Heme degradation / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / dinitrosyl-iron complex binding / glutathione derivative biosynthetic process / glutathione binding / steroid delta-isomerase activity / linoleic acid metabolic process / glutathione peroxidase activity ...Azathioprine ADME / Glutathione conjugation / Heme degradation / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / dinitrosyl-iron complex binding / glutathione derivative biosynthetic process / glutathione binding / steroid delta-isomerase activity / linoleic acid metabolic process / glutathione peroxidase activity / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / xenobiotic catabolic process / epithelial cell differentiation / xenobiotic metabolic process / response to nutrient levels / glutathione metabolic process / fatty acid binding / response to xenobiotic stimulus / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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 SULFONIC ACID / Glutathione S-transferase alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsAdman, E.T. / Le Trong, I. / Stenkamp, R.E. / Nieslanik, B.S. / Dietze, E.C. / Tai, G. / Ibarra, C. / Atkins, W.M.
CitationJournal: Proteins / Year: 2001
Title: Localization of the C-terminus of rat glutathione S-transferase A1-1: crystal structure of mutants W21F and W21F/F220Y.
Authors: Adman, E.T. / Le Trong, I. / Stenkamp, R.E. / Nieslanik, B.S. / Dietze, E.C. / Tai, G. / Ibarra, C. / Atkins, W.M.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE A1-1
C: GLUTATHIONE S-TRANSFERASE A1-1
D: GLUTATHIONE S-TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7979
Polymers76,4433
Non-polymers1,3546
Water5,026279
1
A: GLUTATHIONE S-TRANSFERASE A1-1
hetero molecules

A: GLUTATHIONE S-TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,9622
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5280 Å2
ΔGint-51 kcal/mol
Surface area20150 Å2
MethodPISA
2
C: GLUTATHIONE S-TRANSFERASE A1-1
D: GLUTATHIONE S-TRANSFERASE A1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8656
Polymers50,9622
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-48 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.6, 275.2, 70.3
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailschain A forms crystallographic dimer chains C&D form non-crystallographic dimer

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE A1-1


Mass: 25480.885 Da / Num. of mol.: 3 / Mutation: W21F/F220Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PKKGTB34-W21F / Production host: Escherichia coli (E. coli) / References: UniProt: P00502, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N3O9S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M HEPES, 60% saturated ammonium sulfate, 1 mM S-hexyl glutathione , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1drop
21 mMS-hexyl-glutathione1drop
360 %satammonium sulfate1drop
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 61093 / Num. obs: 58664 / % possible obs: 77 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.6
Reflection shellResolution: 1.8→1.88 Å / Rmerge(I) obs: 0.3 / % possible all: 15.3
Reflection
*PLUS
Highest resolution: 1.88 Å / % possible obs: 85 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 1.98 Å / % possible obs: 45 % / Num. unique obs: 4452 / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→20 Å / σ(F): 5 / σ(I): 5 / Stereochemistry target values: Engh & Humber
Details: XPLOR version 3.8 used bulk solvent correction (KSOL=0.8, BSOL = 20.) anisotropic overall B correction -3.0,2.2,0.84
RfactorNum. reflectionSelection details
Rfree0.285 3846 10% of data
Rwork0.218 --
all-40698 -
obs-38243 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5236 0 84 279 5599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg2.2
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 19.8 Å / σ(F): 5 / % reflection Rfree: 10 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.286
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.2

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