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- PDB-7dw4: Crystal structure of a glutathione S-transferase mutant SbGSTU6(I... -

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Basic information

Entry
Database: PDB / ID: 7dw4
TitleCrystal structure of a glutathione S-transferase mutant SbGSTU6(I55T) from Salix babylonica in complex with glutathione
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / Enzyme / Complex
Function / homology
Function and homology information


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 / 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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase
Similarity search - Component
Biological speciesSalix babylonica (weeping willow)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 mutant SbGSTU6(I55T) 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6502
Polymers26,3431
Non-polymers3071
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-4 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.379, 104.379, 53.126
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-432-

HOH

21A-510-

HOH

31A-534-

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: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.17 Å3/Da / Density % sol: 61.15 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Magnesium acetate tetrahydrate, Sodium cacodylate trihydrate, PEG8000

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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 PILATUS3 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: 1.57→34.42 Å / Num. obs: 46154 / % possible obs: 99.4 % / Redundancy: 1 % / Biso Wilson estimate: 26.78 Å2 / CC1/2: 1 / Net I/σ(I): 1.74
Reflection shellResolution: 1.57→1.91 Å / Num. unique obs: 4387 / 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: 7DW3

7dw3


Resolution: 1.57→34.42 Å / SU ML: 0.171 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1675
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 1990 4.32 %
Rwork0.2195 44107 -
obs0.2198 46097 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.27 Å2
Refinement stepCycle: LAST / Resolution: 1.57→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 20 159 1912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01061797
X-RAY DIFFRACTIONf_angle_d1.17442431
X-RAY DIFFRACTIONf_chiral_restr0.0773264
X-RAY DIFFRACTIONf_plane_restr0.0073309
X-RAY DIFFRACTIONf_dihedral_angle_d20.6206663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.30431260.32412940X-RAY DIFFRACTION93.16
1.61-1.660.29621360.27883148X-RAY DIFFRACTION99.61
1.66-1.710.32611400.27553122X-RAY DIFFRACTION99.85
1.71-1.760.26681420.25173127X-RAY DIFFRACTION99.79
1.76-1.820.29381430.25243157X-RAY DIFFRACTION99.64
1.82-1.90.25251440.23753127X-RAY DIFFRACTION99.91
1.9-1.980.27661430.23953161X-RAY DIFFRACTION99.91
1.98-2.090.26171460.23033135X-RAY DIFFRACTION100
2.09-2.220.2731420.2293172X-RAY DIFFRACTION99.91
2.22-2.390.22191450.21913153X-RAY DIFFRACTION99.97
2.39-2.630.19991440.22753159X-RAY DIFFRACTION99.91
2.63-3.010.28391500.22483183X-RAY DIFFRACTION99.91
3.01-3.790.21731480.21153224X-RAY DIFFRACTION100
3.79-34.420.17971410.19813299X-RAY DIFFRACTION99.54

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