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- PDB-2r3x: Crystal structure of an R15L hGSTA1-1 mutant complexed with S-hex... -

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Basic information

Entry
Database: PDB / ID: 2r3x
TitleCrystal structure of an R15L hGSTA1-1 mutant complexed with S-hexyl-glutathione
ComponentsGlutathione S-transferase A1
KeywordsTRANSFERASE / human Alpha class glutathione transferase 1-1 / S-hexyl glutathione / X-ray crystal structure
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
S-HEXYLGLUTATHIONE / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBurke, J.P.W.G. / Kinsley, N. / Sayed, M. / Sewell, T. / Dirr, H.W.
CitationJournal: Biophys.Chem. / Year: 2010
Title: Arginine 15 stabilizes an S(N)Ar reaction transition state and the binding of anionic ligands at the active site of human glutathione transferase A1-1.
Authors: Gildenhuys, S. / Dobreva, M. / Kinsley, N. / Sayed, Y. / Burke, J. / Pelly, S. / Gordon, G.P. / Sayed, M. / Sewell, T. / Dirr, H.W.
History
DepositionAug 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 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

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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)52,0374
Polymers51,2522
Non-polymers7852
Water12,989721
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.103, 93.858, 51.566
Angle α, β, γ (deg.)90.000, 93.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-5151-

HOH

21B-5224-

HOH

31B-5398-

HOH

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Components

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


Mass: 25626.084 Da / Num. of mol.: 2 / Mutation: R15L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSTA1 / Plasmid: pKHA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08263, glutathione transferase
#2: Chemical ChemComp-GTX / S-HEXYLGLUTATHIONE


Mass: 392.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H30N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: A 4uL hanging drop comprising: 2uL 14 mg/mL R15L hGSTA1-1 solution added to 2uL reservoir buffer (5mM S-hexyl-glutathione, 0.1M TrisHCl, pH 7.5, 10 mM DTT, 15% PEG 4000) was left to ...Details: A 4uL hanging drop comprising: 2uL 14 mg/mL R15L hGSTA1-1 solution added to 2uL reservoir buffer (5mM S-hexyl-glutathione, 0.1M TrisHCl, pH 7.5, 10 mM DTT, 15% PEG 4000) was left to equilibrate in a sealed 24 plate well with 1 mL of reservoir buffer. Crystals were grown for 3 days before harvesting, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 13, 2006
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→19.681 Å / Num. all: 43464 / Num. obs: 39503

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1K3L

1k3l


Resolution: 1.8→18.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.623 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1993 5 %RANDOM
Rwork0.192 ---
obs0.195 39503 90.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.39 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 52 721 4345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223694
X-RAY DIFFRACTIONr_angle_refined_deg1.4562.0214961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6375438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84424.14157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74515722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9711522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022702
X-RAY DIFFRACTIONr_nbd_refined0.2060.22060
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22493
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2710.2548
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.227
X-RAY DIFFRACTIONr_mcbond_it0.9031.52305
X-RAY DIFFRACTIONr_mcangle_it1.34723557
X-RAY DIFFRACTIONr_scbond_it2.30931605
X-RAY DIFFRACTIONr_scangle_it3.4484.51404
LS refinement shellResolution: 1.8→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 127 -
Rwork0.348 2573 -
all-2700 -
obs--83.93 %

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