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- PDB-2cai: Structure of Glutathione-S-Transferase mutant, R21L, from Schisto... -

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Basic information

Entry
Database: PDB / ID: 2cai
TitleStructure of Glutathione-S-Transferase mutant, R21L, from Schistosoma Haematobium
ComponentsGLUTATHIONE S-TRANSFERASE 28 KDA
KeywordsTRANSFERASE / GLUTATHIONE S-TRANSFERASE / HOMODIMER / THIOREDOXIN-LIKE FOLD / DETOXIFICATION / 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, 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. ...Glutathione S-transferase, C-terminal domain / : / 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
BETA-MERCAPTOETHANOL / Glutathione S-transferase class-mu 28 kDa isozyme
Similarity search - Component
Biological speciesSCHISTOSOMA HAEMATOBIUM (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsBaiocco, P. / Gourlay, L.J. / Angelucci, F. / Bellelli, A. / Brunori, M. / Miele, A.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Probing the Mechanism of Gsh Activation in Schistosoma Haematobium Glutathione-S-Transferase by Site-Directed Mutagenesis and X-Ray Crystallography.
Authors: Baiocco, P. / Gourlay, L.J. / Angelucci, F. / Fontaine, J. / Herve, M. / Miele, A.E. / Trottein, F. / Brunori, M. / Bellelli, A.
History
DepositionDec 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE 28 KDA
B: GLUTATHIONE S-TRANSFERASE 28 KDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,56318
Polymers47,7852
Non-polymers1,77816
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)148.716, 148.716, 148.716
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein GLUTATHIONE S-TRANSFERASE 28 KDA / GST 28 / GST CLASS-SIGMA


Mass: 23892.709 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHISTOSOMA HAEMATOBIUM (invertebrata) / Plasmid: PET-23D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30113, glutathione transferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIMPORTANT ROLE IN THE PARASITE DETOXIFICATION SYSTEM ENGINEERED RESIDUE IN CHAIN A, ARG 21 TO LEU ...IMPORTANT ROLE IN THE PARASITE DETOXIFICATION SYSTEM ENGINEERED RESIDUE IN CHAIN A, ARG 21 TO LEU ENGINEERED RESIDUE IN CHAIN B, ARG 21 TO LEU

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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: 2.68 Å3/Da / Density % sol: 53.83 %
Crystal growpH: 7.4
Details: 10% PEG200, PBS PH7.4, 5MM MERCAPTOETHANOL, pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. obs: 25780 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 22 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 20.8 % / Mean I/σ(I) obs: 9.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE7

1oe7


Resolution: 2.26→105.41 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.793 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1309 5.1 %RANDOM
Rwork0.215 ---
obs0.218 24373 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.25 Å2
Refinement stepCycle: LAST / Resolution: 2.26→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 101 183 3602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9924707
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82324.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34815647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1811516
X-RAY DIFFRACTIONr_chiral_restr0.1060.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022495
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21878
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22350
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.2132
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8181.52139
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37523371
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9631506
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0594.51336
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 97
Rwork0.223 1769

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