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- PDB-1m99: Crystal structure of the 26 kDa glutathione S-transferase from Sc... -

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Basic information

Entry
Database: PDB / ID: 1m99
TitleCrystal structure of the 26 kDa glutathione S-transferase from Schistosoma japonicum complexed with glutathione sulfonic acid
ComponentsGlutathione S-Transferase 26kDa
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
GLUTATHIONE SULFONIC ACID / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,8902
Polymers25,5351
Non-polymers3551
Water2,126118
1
A: Glutathione S-Transferase 26kDa
hetero molecules

A: Glutathione S-Transferase 26kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7804
Polymers51,0692
Non-polymers7112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z1
Buried area4000 Å2
ΔGint-20 kcal/mol
Surface area19550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.07, 115.07, 78.28
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-336-

HOH

21A-385-

HOH

31A-398-

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 26kDa / 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-GTS / GLUTATHIONE SULFONIC ACID


Mass: 355.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.88 Å3/Da / Density % sol: 56.95 %
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 24, 1996
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→32 Å / Num. all: 14209 / Num. obs: 14209 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 28.5 Å2 / Rsym value: 0.097 / Net I/σ(I): 29.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1306 / Rsym value: 0.578 / % possible all: 93.2
Reflection
*PLUS
Lowest resolution: 26 Å / Num. measured all: 137582 / Rmerge(I) obs: 0.097
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.578

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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: 2.3→26 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1815524.16 / Data cutoff high rms absF: 1815524.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Pro217 and Lys218 were disordered and not included in this entry
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1427 10.2 %RANDOM
Rwork0.218 ---
all-14031 --
obs-14031 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.08 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.95 Å26.61 Å20 Å2
2--5.95 Å20 Å2
3----11.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 23 118 1919
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 232 10.2 %
Rwork0.255 2038 -
obs-2270 99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SLFGSH.PARAMSLFGSH.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.3 Å / % 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
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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