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- PDB-1u87: Crystal Structure Of The 26 Kda Glutathione S-Transferase Y7F mut... -

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Basic information

Entry
Database: PDB / ID: 1u87
TitleCrystal Structure Of The 26 Kda Glutathione S-Transferase Y7F mutant From Schistosoma Japonicum Complexed With Glutathione
ComponentsGlutathione S-Transferase 26 kDa
KeywordsTRANSFERASE
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
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 / 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, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
GLUTATHIONE / 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 1.3Mar 21, 2012Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.5Nov 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 1.6Oct 25, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,8262
Polymers25,5191
Non-polymers3071
Water0
1
A: Glutathione S-Transferase 26 kDa
hetero molecules

A: Glutathione S-Transferase 26 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6524
Polymers51,0372
Non-polymers6152
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-11
Unit cell
Length a, b, c (Å)123.050, 123.050, 72.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 25518.721 Da / Num. of mol.: 1 / 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-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S

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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: 3 Å3/Da / Density % sol: 59 %
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: Aug 23, 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→30 Å / Num. obs: 6781 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.17 / Rsym value: 0.16 / Net I/σ(I): 4
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.59 / Num. unique all: 4301 / Rsym value: 0.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gta

1gta


Resolution: 3.5→29.56 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 278455.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 687 10.1 %RANDOM
Rwork0.199 ---
all0.21 ---
obs0.199 6094 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.240364 e/Å3
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å25.46 Å20 Å2
2--3.19 Å20 Å2
3----6.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 20 0 1749
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.92
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.952.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 85 8.8 %
Rwork0.21 880 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GSH.PARAMGSH.TOP

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