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- PDB-1m9b: Crystal structure of the 26 kDa glutathione S-transferase from Sc... -

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Basic information

Entry
Database: PDB / ID: 1m9b
TitleCrystal structure of the 26 kDa glutathione S-transferase from Schistosoma japonicum complexed with gamma-glutamyl[S-(2-iodobenzyl)cysteinyl]glycine
ComponentsGlutathione S-Transferase 26 kDa
KeywordsTRANSFERASE / Glutathione Transferase / antigen / multigene family
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process
Similarity search - Function
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, 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
GAMMA-GLUTAMYL[S-(2-IODOBENZYL)CYSTEINYL]GLYCINE / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCardoso, R.M.F. / Daniels, D.S. / Bruns, C.M. / Tainer, J.A.
Citation
Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2003
Title: Characterization of the electrophile binding site and substrate binding mode of the 26-kDa glutathione S-transferase from Schistosoma japonicum
Authors: Cardoso, R.M.F. / Daniels, D.S. / Bruns, C.M. / Tainer, J.A.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structures of a schistosomal drug and vaccine target: glutathione S-transferase from Schistosoma japonica and its complex with the leading antischistosomal drug praziquantel
Authors: McTigue, M.A. / Williams, D.R. / Tainer, J.A.
#2: Journal: Protein Sci. / Year: 1994
Title: Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV
Authors: Lim, K. / Ho, J.X. / Keeling, K. / Gilliland, G.L. / Ji, X. / Ruker, F. / Carter, D.C.
History
DepositionJul 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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

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Assembly

Deposited unit
A: Glutathione S-Transferase 26 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0582
Polymers25,5351
Non-polymers5231
Water1,22568
1
A: Glutathione S-Transferase 26 kDa
hetero molecules

A: Glutathione S-Transferase 26 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1164
Polymers51,0692
Non-polymers1,0472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z1
Buried area4660 Å2
ΔGint-23 kcal/mol
Surface area19520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.567, 116.567, 78.748
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-359-

HOH

DetailsThere is one GST subunit per asymmetric unit and the second subunit of the GST dimer is generated by the symmetry operation: -x, -x+y, -z

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Components

#1: Protein Glutathione S-Transferase 26 kDa / GST 26 / SJ26 antigen


Mass: 25534.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Plasmid: pGEX-3X / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, glutathione transferase
#2: Chemical ChemComp-IBG / GAMMA-GLUTAMYL[S-(2-IODOBENZYL)CYSTEINYL]GLYCINE


Mass: 523.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22IN3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.97 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, ethanol, dithiothrietol, threalose, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
148-50 %satammonium sulfate1reservoir
22 %(v/v)ethanol1reservoir
3225 mMsodium acetate1reservoirpH5.6
410 mMdithiothreitol1reservoir
510 mMthrealose1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1996
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. all: 9743 / Num. obs: 9743 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 46 Å2 / Rsym value: 0.078 / Net I/σ(I): 21.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 871 / Rsym value: 0.689 / % possible all: 89.4
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 26 Å / Num. measured all: 56234 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 89.4 % / Rmerge(I) obs: 0.689

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GTA

1gta


Resolution: 2.6→26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1537461.75 / Data cutoff high rms absF: 1537461.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 937 9.9 %RANDOM
Rwork0.231 ---
all-9507 --
obs-9507 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.62 Å2 / ksol: 0.367458 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.57 Å28.1 Å20 Å2
2--5.57 Å20 Å2
3----11.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 28 68 1874
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.862
X-RAY DIFFRACTIONc_scangle_it3.892.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 107 9 %
Rwork0.303 1088 -
obs-1195 72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2IBG.PARAMIBG.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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