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- PDB-7dw3: Crystal structure of a glutathione S-transferase mutant SbGSTU6(I... -

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Basic information

Entry
Database: PDB / ID: 7dw3
TitleCrystal structure of a glutathione S-transferase mutant SbGSTU6(I55T) from Salix babylonica
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / Enzyme / Complex / Mutant
Function / homology
Function and homology information


response to chemical / glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytosol
Similarity search - Function
Glutathione S-transferases Tau, C-terminal alpha helical domain, plant / Glutathione S-transferase Omega/Tau-like / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Glutathione S-transferase
Similarity search - Component
Biological speciesSalix babylonica (weeping willow)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhuge, X.L. / Yang, H.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC 32071486 China
CitationJournal: To Be Published
Title: Crystal structure of a glutathione S-transferase SbGSTU6 from Salix babylonica in complex with glutathione
Authors: Zhuge, X.L. / Yang, H.L.
History
DepositionJan 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)26,3431
Polymers26,3431
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11440 Å2
Unit cell
Length a, b, c (Å)104.882, 104.882, 53.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

21A-345-

HOH

31A-379-

HOH

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Components

#1: Protein Glutathione S-transferase /


Mass: 26342.508 Da / Num. of mol.: 1 / Mutation: I55T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salix babylonica (weeping willow) / Gene: GSTU6 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y5R032
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.19 Å3/Da / Density % sol: 61.49 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Magnesium acetate tetrahydrate, Sodium cacodylate trihydrate, PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.93→34.51 Å / Num. obs: 25535 / % possible obs: 99.92 % / Redundancy: 1 % / Biso Wilson estimate: 32.59 Å2 / CC1/2: 1 / Net I/σ(I): 1.89
Reflection shellResolution: 1.93→2.06 Å / Num. unique obs: 2513 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DW2

7dw2


Resolution: 1.93→34.51 Å / SU ML: 0.2065 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.9098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 2019 7.91 %
Rwork0.217 23508 -
obs0.2189 25527 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.18 Å2
Refinement stepCycle: LAST / Resolution: 1.93→34.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 0 109 1842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951778
X-RAY DIFFRACTIONf_angle_d1.09782407
X-RAY DIFFRACTIONf_chiral_restr0.0713262
X-RAY DIFFRACTIONf_plane_restr0.0069305
X-RAY DIFFRACTIONf_dihedral_angle_d21.3007659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.32771380.27551671X-RAY DIFFRACTION100
1.98-2.030.31441430.25291650X-RAY DIFFRACTION99.94
2.03-2.090.28941430.24891661X-RAY DIFFRACTION100
2.09-2.160.27861430.23351649X-RAY DIFFRACTION100
2.16-2.240.26541410.21571679X-RAY DIFFRACTION99.89
2.24-2.330.26751440.21571662X-RAY DIFFRACTION100
2.33-2.430.27921460.21811667X-RAY DIFFRACTION100
2.43-2.560.24111480.22641662X-RAY DIFFRACTION99.83
2.56-2.720.28331420.21951668X-RAY DIFFRACTION100
2.72-2.930.25351430.21971702X-RAY DIFFRACTION100
2.93-3.230.21831430.2251664X-RAY DIFFRACTION99.89
3.23-3.690.22891470.20621688X-RAY DIFFRACTION100
3.69-4.650.21911470.19751715X-RAY DIFFRACTION100
4.65-34.510.22281510.21881770X-RAY DIFFRACTION99.84

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