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- PDB-1xwg: Human GST A1-1 T68E mutant -

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Basic information

Entry
Database: PDB / ID: 1xwg
TitleHuman GST A1-1 T68E mutant
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / alpha-beta thioredoxin fold
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 / epithelial cell differentiation / xenobiotic metabolic process / glutathione 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 / 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 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 A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGrahn, E. / Jakobsson, E. / Gustafsson, A. / Novotny, M. / Grehn, L. / Olin, B. / Madsen, D. / Wahlberg, M. / Mannervik, B. / Kleywegt, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: New crystal structures of human glutathione transferase A1-1 shed light on glutathione binding and the conformation of the C-terminal helix.
Authors: Grahn, E. / Novotny, M. / Jakobsson, E. / Gustafsson, A. / Grehn, L. / Olin, B. / Madsen, D. / Wahlberg, M. / Mannervik, B. / Kleywegt, G.J.
History
DepositionNov 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)51,1342
Polymers51,1342
Non-polymers00
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-24 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.077, 90.570, 51.489
Angle α, β, γ (deg.)90.00, 93.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

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Components

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


Mass: 25566.934 Da / Num. of mol.: 2 / Mutation: T68E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08263, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG4 000, DTT, Tris-HCl, MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.996 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.996 Å / Relative weight: 1
ReflectionResolution: 1.85→67 Å / Num. obs: 38714 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0
Reflection shellResolution: 1.85→1.92 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1gsd

1gsd


Resolution: 1.85→67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.853 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21809 3860 10 %RANDOM
Rwork0.16415 ---
obs0.16944 34854 99.87 %-
all-38714 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.978 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å21.14 Å2
2--0.4 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 0 448 4022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223644
X-RAY DIFFRACTIONr_bond_other_d0.0020.023457
X-RAY DIFFRACTIONr_angle_refined_deg1.512.0014899
X-RAY DIFFRACTIONr_angle_other_deg0.90238114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685432
X-RAY DIFFRACTIONr_chiral_restr0.0960.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023884
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02688
X-RAY DIFFRACTIONr_nbd_refined0.2210.2725
X-RAY DIFFRACTIONr_nbd_other0.2360.23763
X-RAY DIFFRACTIONr_nbtor_other0.0850.21940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.219
X-RAY DIFFRACTIONr_mcbond_it0.9521.52184
X-RAY DIFFRACTIONr_mcangle_it1.66123538
X-RAY DIFFRACTIONr_scbond_it2.44331460
X-RAY DIFFRACTIONr_scangle_it4.014.51361
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 277
Rwork0.196 2583

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