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- PDB-2ca8: Structure of Sh28GST in complex with GSH at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 2ca8
TitleStructure of Sh28GST in complex with GSH at pH 6.0
ComponentsGLUTATHIONE S-TRANSFERASE 28 KDA
KeywordsTRANSFERASE / SIGMA CLASS GST / DETOXIFICATION / GLUTATHIONE / PROSTAGLANDIN D2 SYNTHASE
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, 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, C-terminal domain / : / 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
GLUTATHIONE / Glutathione S-transferase class-mu 28 kDa isozyme
Similarity search - Component
Biological speciesSCHISTOSOMA HAEMATOBIUM (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsBaiocco, P. / Gourlay, L.J. / Angelucci, F. / Bellelli, A. / Miele, A.E. / Brunori, M.
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 20, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2Apr 17, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 28 KDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4383
Polymers23,9371
Non-polymers5022
Water90150
1
A: GLUTATHIONE S-TRANSFERASE 28 KDA
hetero molecules

A: GLUTATHIONE S-TRANSFERASE 28 KDA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8776
Polymers47,8732
Non-polymers1,0034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
MethodPISA
Unit cell
Length a, b, c (Å)53.304, 53.304, 142.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

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Components

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


Mass: 23936.746 Da / Num. of mol.: 1
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-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONJUGATION OF REDUCED GLUTATHIONE TO A WIDE NUMBER OF EXOGENOUS AND ENDOGENOUS HYDROPHOBIC ELECTROPHILES.

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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: 2.35 Å3/Da / Density % sol: 47.3 %
Crystal growpH: 6 / Details: 10% PEG4K, 0.2M IMADAZOLE/MALATE PH 6.0

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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: 2.46→20 Å / Num. obs: 8673 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 8.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.59 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 8.7 / % possible all: 98.4

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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: 2.49→47.46 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.76 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.609 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 412 4.8 %RANDOM
Rwork0.203 ---
obs0.206 8261 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.49→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 33 50 1734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221734
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9852335
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22823.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78415321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2491510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.2770
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21164
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.51066
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.321682
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0763747
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2994.5653
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: 2.49→2.55 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 23
Rwork0.244 553

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