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- PDB-6ato: Crystal structure of hGSTA1-1 complexed with GSH and MPD in each ... -

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Basic information

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


Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / 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 ...Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / glutathione derivative biosynthetic process / 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 / 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 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. ...Glutathione S-transferase, alpha class / : / 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 A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsKumari, V. / Ji, X.
Citation
Journal: To be published
Title: The dynamic nature of hGSTA1-1 C-terminal 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 / 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

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)52,52011
Polymers51,0782
Non-polymers1,4429
Water10,269570
1
A: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3196
Polymers25,5391
Non-polymers7805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutathione S-transferase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2015
Polymers25,5391
Non-polymers6624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.675, 90.960, 50.751
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

21A-614-

HOH

31B-522-

HOH

41B-602-

HOH

51B-647-

HOH

61B-667-

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-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.23 Å3/Da / Density % sol: 44.89 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 200 MME, 25% (w/v), 0.1 M Tris HCl, pH 8.5

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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: Apr 8, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 63121 / % possible obs: 97.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.22
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 2.15 / Num. unique all: 5935 / % possible all: 92.1

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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: 1.55→28.976 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.93
RfactorNum. reflection% reflection
Rfree0.2079 1033 1.64 %
Rwork0.1695 --
obs0.1701 63095 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→28.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 96 570 4244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053803
X-RAY DIFFRACTIONf_angle_d0.8295127
X-RAY DIFFRACTIONf_dihedral_angle_d11.0422384
X-RAY DIFFRACTIONf_chiral_restr0.049557
X-RAY DIFFRACTIONf_plane_restr0.017641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5466-1.62810.28611420.22798218X-RAY DIFFRACTION90
1.6281-1.73010.25721370.21279082X-RAY DIFFRACTION100
1.7301-1.86370.22541640.18669122X-RAY DIFFRACTION100
1.8637-2.05120.21361620.17039095X-RAY DIFFRACTION100
2.0512-2.34790.22191300.16239101X-RAY DIFFRACTION99
2.3479-2.95760.18781530.17458878X-RAY DIFFRACTION97
2.9576-28.98070.19371450.15228566X-RAY DIFFRACTION92

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