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- PDB-1k3l: Crystal Structure Analysis of S-hexyl-glutathione Complex of Glut... -

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Basic information

Entry
Database: PDB / ID: 1k3l
TitleCrystal Structure Analysis of S-hexyl-glutathione Complex of Glutathione Transferase at 1.5 Angstroms Resolution
ComponentsGLUTATHIONE S-TRANSFERASE A1
KeywordsTRANSFERASE / glutathione S-transferase / S-hexyl glutathione / water structure
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 / epithelial cell differentiation / glutathione metabolic process / 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 / 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 / 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
S-HEXYLGLUTATHIONE / Glutathione S-transferase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLe Trong, I. / Stenkamp, R.E. / Ibarra, C. / Atkins, W.M. / Adman, E.T.
CitationJournal: Proteins / Year: 2002
Title: 1.3-A resolution structure of human glutathione S-transferase with S-hexyl glutathione bound reveals possible extended ligandin binding site
Authors: Le Trong, I. / Stenkamp, R.E. / Ibarra, C. / Atkins, W.M. / Adman, E.T.
History
DepositionOct 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)51,8634
Polymers51,0782
Non-polymers7852
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-35 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.960, 93.994, 51.872
Angle α, β, γ (deg.)90.00, 92.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-6151-

HOH

21A-6359-

HOH

31B-6154-

HOH

41B-6394-

HOH

51B-6405-

HOH

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE A1 / GSTA1-1


Mass: 25538.924 Da / Num. of mol.: 2
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: 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.: 477 / 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: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG3350, 0.1 M Tris-Cl pH 7.5, 10mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
218 %PEG33501reservoir
30.1 MTris-Cl1reservoirpH7.5
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. all: 75496 / Num. obs: 75496 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.444 / % possible all: 94.2
Reflection
*PLUS
Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 94.2 % / Num. unique obs: 7153 / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GSE [LIGANDS AND WATER REMOVED]

1gse


Resolution: 1.5→10 Å / Num. parameters: 37081 / Num. restraintsaints: 44934 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 3761 5 %RANDOM
Rwork0.1575 ---
all0.1654 75227 --
obs0.1654 75227 99.2 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 3725 / Occupancy sum non hydrogen: 4094
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 52 477 4122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0242
X-RAY DIFFRACTIONs_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.024
X-RAY DIFFRACTIONs_approx_iso_adps0.088
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor all: 0.1654 / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.158

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