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- PDB-5ld0: Chimeric GST -

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Basic information

Entry
Database: PDB / ID: 5ld0
TitleChimeric GST
ComponentsGlutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1
KeywordsTRANSFERASE / Directed evolution / Glutathione transferase A1-1 / protein stability
Function / homology
Function and homology information


Azathioprine ADME / Glutathione conjugation / response to stilbenoid / Heme degradation / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / : / dinitrosyl-iron complex binding / glutathione binding / glutathione derivative biosynthetic process / steroid delta-isomerase activity ...Azathioprine ADME / Glutathione conjugation / response to stilbenoid / Heme degradation / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / : / dinitrosyl-iron complex binding / glutathione binding / glutathione derivative biosynthetic process / steroid delta-isomerase activity / linoleic acid metabolic process / Glutathione conjugation / glutathione peroxidase activity / Azathioprine ADME / Heme degradation / NFE2L2 regulating anti-oxidant/detoxification enzymes / prostaglandin metabolic process / glutathione transferase / glutathione transferase activity / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / glutathione metabolic process / xenobiotic catabolic process / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / response to bacterium / 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 transferase family / 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 ...Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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 S-transferase alpha-2 / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAxarli, A. / Muleta, A.W. / Chronopoulou, E.G. / Papageorgiou, A.C. / Labrou, N.E.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Directed evolution of glutathione transferases towards a selective glutathione-binding site and improved oxidative stability.
Authors: Axarli, I. / Muleta, A.W. / Chronopoulou, E.G. / Papageorgiou, A.C. / Labrou, N.E.
History
DepositionJun 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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 A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8162
Polymers25,7801
Non-polymers351
Water5,062281
1
A: Glutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1
hetero molecules

A: Glutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6314
Polymers51,5602
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area3540 Å2
ΔGint-63 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 90.900, 82.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21A-617-

HOH

31A-661-

HOH

41A-662-

HOH

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Components

#1: Protein Glutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1 / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1 / GST 1b-1b / GST A2-2 / ...GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1 / GST 1b-1b / GST A2-2 / Glutathione S-transferase Ya-2 / GST Ya2 / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1


Mass: 25780.139 Da / Num. of mol.: 1
Fragment: UNP residues 1-85,UNP residues 86-213,UNP residues 214-222
Source method: isolated from a genetically manipulated source
Details: Chimeric protein from gene shuffling of rat and human GSTA1-1
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: GSTA1, Gsta2 / Production host: Escherichia coli (E. coli)
References: UniProt: P08263, UniProt: P04903, glutathione transferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: Sodium formate 0.15 M, PEG 4000 15% (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 28561 / % possible obs: 96.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.052 / Net I/σ(I): 16.95
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 1768 / CC1/2: 0.497 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PKZ

1pkz


Resolution: 1.6→19.277 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 1476 5.17 %
Rwork0.1728 --
obs0.1742 28535 96.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→19.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 1 281 1952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061712
X-RAY DIFFRACTIONf_angle_d0.8982305
X-RAY DIFFRACTIONf_dihedral_angle_d15.3161070
X-RAY DIFFRACTIONf_chiral_restr0.05256
X-RAY DIFFRACTIONf_plane_restr0.005293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.65170.33541120.3262054X-RAY DIFFRACTION82
1.6517-1.71070.31151300.25652339X-RAY DIFFRACTION94
1.7107-1.77910.2521430.21212496X-RAY DIFFRACTION100
1.7791-1.860.241430.19962510X-RAY DIFFRACTION100
1.86-1.9580.23731530.19412481X-RAY DIFFRACTION100
1.958-2.08060.18981430.16682531X-RAY DIFFRACTION100
2.0806-2.2410.21931490.15872492X-RAY DIFFRACTION99
2.241-2.46610.19361120.16432555X-RAY DIFFRACTION99
2.4661-2.8220.17991170.1722538X-RAY DIFFRACTION99
2.822-3.55180.18811400.16462530X-RAY DIFFRACTION98
3.5518-19.27850.17441340.15562533X-RAY DIFFRACTION94

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