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- PDB-7dwg: Crystal structure of a glutathione S-transferase mutant SbGSTU7(T... -

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Basic information

Entry
Database: PDB / ID: 7dwg
TitleCrystal structure of a glutathione S-transferase mutant SbGSTU7(T53I) 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 transferase family / 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: 1.67 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 SbGSTU7(T53I) from Salix babylonica in complex with glutathione
Authors: Zhuge, X.L. / Yang, H.L.
History
DepositionJan 17, 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)25,9332
Polymers25,6251
Non-polymers3071
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-4 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.148, 55.148, 184.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

21A-464-

HOH

31A-581-

HOH

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Components

#1: Protein Glutathione S-transferase


Mass: 25625.475 Da / Num. of mol.: 1 / Mutation: T53I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salix babylonica (weeping willow) / Gene: GSTU7 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Y5R087
#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.: 183 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: HEPES sodium, PEG 400, Ammonium sulfate

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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: 1.67→35.34 Å / Num. obs: 34121 / % possible obs: 99.84 % / Redundancy: 1 % / Biso Wilson estimate: 29.49 Å2 / CC1/2: 1 / Net I/σ(I): 2.69
Reflection shellResolution: 1.67→1.73 Å / Num. unique obs: 3335 / 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: 7DWE

7dwe


Resolution: 1.67→35.34 Å / SU ML: 0.1489 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2247 1996 5.85 %
Rwork0.2073 32125 -
obs0.2083 34121 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.29 Å2
Refinement stepCycle: LAST / Resolution: 1.67→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 20 183 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01221757
X-RAY DIFFRACTIONf_angle_d1.182384
X-RAY DIFFRACTIONf_chiral_restr0.0759259
X-RAY DIFFRACTIONf_plane_restr0.0071300
X-RAY DIFFRACTIONf_dihedral_angle_d17.9668648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.25951390.25192236X-RAY DIFFRACTION99.66
1.71-1.760.29761390.24372230X-RAY DIFFRACTION100
1.76-1.810.25561400.23672244X-RAY DIFFRACTION99.79
1.81-1.870.21831400.22552260X-RAY DIFFRACTION99.79
1.87-1.930.27441380.23712247X-RAY DIFFRACTION99.83
1.93-2.010.25461410.23082259X-RAY DIFFRACTION99.88
2.01-2.10.22341410.21132271X-RAY DIFFRACTION99.96
2.1-2.210.24191420.20932290X-RAY DIFFRACTION100
2.21-2.350.25391400.2052262X-RAY DIFFRACTION100
2.35-2.530.24671440.21422308X-RAY DIFFRACTION99.96
2.53-2.790.21821450.22192308X-RAY DIFFRACTION99.8
2.79-3.190.24331430.21582309X-RAY DIFFRACTION100
3.19-4.020.20051480.19892381X-RAY DIFFRACTION100
4.02-35.340.20621560.19022520X-RAY DIFFRACTION99.37

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