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- PDB-1u88: Crystal Structure Of The 26 Kda Glutathione S-Transferase Y7F mut... -

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Basic information

Entry
Database: PDB / ID: 1u88
TitleCrystal Structure Of The 26 Kda Glutathione S-Transferase Y7F mutant From Schistosoma Japonicum Complexed With S-Octyl Glutathione
ComponentsGlutathione S-transferase 26 kDa
KeywordsTRANSFERASE
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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...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 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-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
L-GAMMA-GLUTAMYL-S-OCTYL-D-CYSTEINYLGLYCINE / Glutathione S-transferase class-mu 26 kDa isozyme
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSmith, A.W. / Camara-Artigas, A.
CitationJournal: Biochemistry / Year: 2005
Title: Crystallographic and Thermodynamic Analysis of the Binding of S-Octylglutathione to the Tyr 7 to Phe Mutant of Glutathione S-Transferase from Schistosoma japonicum(,)
Authors: Andujar-Sanchez, M. / Smith, A.W. / Clemente-Jimenez, J.M. / Rodriguez-Vico, F. / Las Heras-Vazquez, F.J. / Jara-Perez, V. / Camara-Artigas, A.
History
DepositionAug 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 1.4Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Glutathione S-transferase 26 kDa
B: Glutathione S-transferase 26 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4573
Polymers51,0372
Non-polymers4201
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-22 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.100, 116.100, 73.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Glutathione S-transferase 26 kDa / Glutathione S-transferase


Mass: 25518.721 Da / Num. of mol.: 2 / Mutation: Y7F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: P08515, glutathione transferase
#2: Chemical ChemComp-GTY / L-GAMMA-GLUTAMYL-S-OCTYL-D-CYSTEINYLGLYCINE / S-OCTYLGLUTATHIONE


Mass: 419.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H33N3O6S

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M sodium citrate, 2M ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 17, 2003 / Details: Osmic confocal mirror assembly
RadiationMonochromator: Osmic confocal mirror assembly / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 6280 / % possible obs: 82.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.12 / Net I/σ(I): 5.7
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.47 / Num. unique all: 2155 / Rsym value: 0.37 / % possible all: 82.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GlutathioneS-transferase Y7F mutant from Schistosoma Japonicum

Resolution: 3.5→19.73 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 201391.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.317 354 5.6 %RANDOM
Rwork0.22 ---
obs0.22 5926 87.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.802 Å2 / ksol: 0.23025 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å25.04 Å20 Å2
2--1.26 Å20 Å2
3----2.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.28 Å
Refinement stepCycle: LAST / Resolution: 3.5→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 28 0 3486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 69 6.4 %
Rwork0.229 1003 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GTY.PARAMGTY.TOP

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