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- PDB-6atr: Crystal structure of hGSTA1-1 complexed with two GSH analogues in... -

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Basic information

Entry
Database: PDB / ID: 6atr
TitleCrystal structure of hGSTA1-1 complexed with two GSH analogues in each subunit
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / Glutathione S-transferase / glutathione transferase
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / 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 ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / 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 / epithelial cell differentiation / xenobiotic metabolic process / fatty acid binding / extracellular exosome / cytosol
Similarity search - Function
Glutathione S-transferase, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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, alpha class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / 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
L-gamma-glutamyl-L-alanylglycine / Chem-GSN / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.29 Å
AuthorsKumari, V. / Ji, X.
Citation
Journal: To be published
Title: hGSTA1 apo structure and dynamic c-terminus helix
Authors: Kumari, V. / Ji, X.
#1: Journal: J. Mol. Biol. / Year: 1993
Title: Structure determination and refinement of human alpha class glutathione transferase A1-1, and a comparison with the Mu and Pi class enzymes.
Authors: Sinning, I. / Kleywegt, G.J. / Cowan, S.W. / Reinemer, P. / Dirr, H.W. / Huber, R. / Gilliland, G.L. / Armstrong, R.N. / Ji, X. / Board, P.G.
History
DepositionAug 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione S-transferase A1
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,16620
Polymers51,0782
Non-polymers2,08818
Water15,385854
1
A: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,70712
Polymers25,5391
Non-polymers1,16811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4598
Polymers25,5391
Non-polymers9207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.163, 94.487, 51.782
Angle α, β, γ (deg.)90.00, 92.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-670-

HOH

21A-708-

HOH

31B-631-

HOH

41B-672-

HOH

51B-778-

HOH

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Components

#1: Protein Glutathione S-transferase A1 / / GST HA subunit 1 / GST class-alpha member 1 / GST-epsilon / GSTA1-1 / GTH1


Mass: 25538.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pET30b(+)hGSTA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-BWS / L-gamma-glutamyl-L-alanylglycine


Mass: 275.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H17N3O6
#3: Chemical ChemComp-GSN / 2-AMINO-5-[1-(CARBOXYLATOMETHYLCARBAMOYL)-2-NITROSOSULFANYL-ETHYL]AMINO-5-OXO-PENTANOATE / S-NITROSOGLUTATHIONE / S-NITROSO GAMMA-GLUTAMYLCYSTEINYLGLYCINE / S-Nitrosoglutathione


Mass: 334.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O7S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 48.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 2000 MME, 25% (w/v), 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→30 Å / Num. obs: 113271 / % possible obs: 93.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.52
Reflection shellResolution: 1.29→1.34 Å / Rmerge(I) obs: 0.733 / Num. unique obs: 7770 / % possible all: 64.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GUH

1guh


Resolution: 1.29→22.899 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.22
RfactorNum. reflection% reflection
Rfree0.1823 1003 0.89 %
Rwork0.1683 --
obs0.1684 113023 93.6 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 1.29→22.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 138 854 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074305
X-RAY DIFFRACTIONf_angle_d1.0235823
X-RAY DIFFRACTIONf_dihedral_angle_d12.8761733
X-RAY DIFFRACTIONf_chiral_restr0.076614
X-RAY DIFFRACTIONf_plane_restr0.006773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2896-1.35750.37831100.346811566X-RAY DIFFRACTION68
1.3575-1.44260.30761400.288815526X-RAY DIFFRACTION91
1.4426-1.55390.26241470.230316712X-RAY DIFFRACTION98
1.5539-1.71030.19371460.173316948X-RAY DIFFRACTION99
1.7103-1.95760.17221580.156316983X-RAY DIFFRACTION100
1.9576-2.4660.15191490.146717106X-RAY DIFFRACTION100
2.466-22.90250.15751530.145717179X-RAY DIFFRACTION100

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