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- PDB-2f8f: Crystal structure of the Y10F mutant of the gluathione s-transfer... -

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Basic information

Entry
Database: PDB / ID: 2f8f
TitleCrystal structure of the Y10F mutant of the gluathione s-transferase from schistosoma haematobium
ComponentsGlutathione S-transferase 28 kDa
KeywordsTRANSFERASE / thioredoxin fold / homodimer / protein_GTT complex
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
GLUTATHIONE / Glutathione S-transferase class-mu 28 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma haematobium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGourlay, L.J. / Baiocco, P. / Angelucci, F. / Miele, A.E. / Bellelli, A. / 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 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 18, 2012Group: Non-polymer description
Revision 1.4Mar 21, 2012Group: Non-polymer description
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Glutathione S-transferase 28 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4564
Polymers47,8412
Non-polymers6152
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-14 kcal/mol
Surface area20170 Å2
MethodPISA
2
A: Glutathione S-transferase 28 kDa
hetero molecules

B: Glutathione S-transferase 28 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4564
Polymers47,8412
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area3480 Å2
ΔGint-22 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.227, 77.594, 53.143
Angle α, β, γ (deg.)90.00, 94.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutathione S-transferase 28 kDa / GST 28 / GST class- mu


Mass: 23920.746 Da / Num. of mol.: 2 / Mutation: Y10F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma haematobium (invertebrata) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/plys / References: UniProt: P30113, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium sulphate 2.1 M, 100 mM tris, 5mM b-mercaptoethanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.993→53.452 Å / Num. all: 29514 / Num. obs: 23175 / % possible obs: 96.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.154 Å / % possible all: 98.81

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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: 2.1→53.45 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.18 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28751 1231 5 %RANDOM
Rwork0.22097 ---
obs0.22423 23175 96.64 %-
all-29514 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.081 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å22.32 Å2
2---1.89 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 40 148 3407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223355
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9774533
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1695404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87224.558147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10615617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0051515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022473
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21612
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22282
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3450.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7981.52102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35223283
X-RAY DIFFRACTIONr_scbond_it1.70831428
X-RAY DIFFRACTIONr_scangle_it2.5934.51250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 90 -
Rwork0.231 1738 -
obs--98.81 %

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