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- PDB-5lcz: Chimeric GST -

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Basic information

Entry
Database: PDB / ID: 5lcz
TitleChimeric GST
ComponentsGlutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione 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 derivative biosynthetic process / glutathione binding / linoleic acid metabolic 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 derivative biosynthetic process / glutathione binding / linoleic acid metabolic process / steroid Delta-isomerase activity / 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 / xenobiotic catabolic process / epithelial cell differentiation / glutathione metabolic process / xenobiotic metabolic process / fatty acid binding / response to bacterium / mitochondrion / 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 / 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 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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 / 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: 2.325 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 / 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,Glutathione S-transferase alpha-2,Glutathione S-transferase A1
B: Glutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1,Glutathione S-transferase alpha-2,Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8683
Polymers51,5602
Non-polymers3071
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-25 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.920, 91.380, 51.490
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutathione S-transferase A1,Glutathione S-transferase alpha-2,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 / 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.: 2
Fragment: UNP residues 1-54,UNP residues 54-65,UNP residues 66-85,UNP residues 86-213,UNP residues 214-222
Source method: isolated from a genetically manipulated source
Details: Protein obtained after gene shuffling of human and rat 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-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG 4000 20% (w/v), ammonium citrate 0.2 M, pH 6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8081 Å / Relative weight: 1
ReflectionResolution: 2.32→20 Å / Num. obs: 19517 / % possible obs: 98.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 51.4 Å2 / CC1/2: 0.992 / Rsym value: 0.0112 / Net I/σ(I): 9.04
Reflection shellResolution: 2.32→2.39 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.3 / % possible all: 83.4

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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: 1pkw

1pkw


Resolution: 2.325→19.669 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 31.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2683 974 4.99 %
Rwork0.2003 --
obs0.2036 19502 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.325→19.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 20 118 3409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083353
X-RAY DIFFRACTIONf_angle_d1.044506
X-RAY DIFFRACTIONf_dihedral_angle_d13.9312079
X-RAY DIFFRACTIONf_chiral_restr0.049499
X-RAY DIFFRACTIONf_plane_restr0.006573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3251-2.44750.41971310.30132503X-RAY DIFFRACTION94
2.4475-2.60050.32121400.25762662X-RAY DIFFRACTION100
2.6005-2.80080.3361380.24812649X-RAY DIFFRACTION100
2.8008-3.08170.27931400.23752669X-RAY DIFFRACTION100
3.0817-3.52540.29551400.20782660X-RAY DIFFRACTION100
3.5254-4.43320.21961410.16592675X-RAY DIFFRACTION100
4.4332-19.66960.23941440.17212710X-RAY DIFFRACTION100

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