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

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Basic information

Entry
Database: PDB / ID: 7dwf
TitleCrystal structure of a glutathione S-transferase mutant SbGSTU7(T53I) from Salix babylonica
ComponentsGlutathione S-transferase
KeywordsTRANSFERASE / Enzyme
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 S-transferase
Similarity search - Component
Biological speciesSalix babylonica (weeping willow)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
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
B: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)51,2512
Polymers51,2512
Non-polymers00
Water1,802100
1
A: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)25,6251
Polymers25,6251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)25,6251
Polymers25,6251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.055, 55.055, 182.635
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein Glutathione S-transferase


Mass: 25625.475 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: HEPES sodium, PEG400, 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: 2.21→29.62 Å / Num. obs: 26786 / % possible obs: 98.88 % / Redundancy: 1 % / Biso Wilson estimate: 41.2 Å2 / CC1/2: 1 / Net I/σ(I): 6.03
Reflection shellResolution: 2.21→2.29 Å / Num. unique obs: 2565 / 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: 7DWD

7dwd


Resolution: 2.21→29.62 Å / SU ML: 0.2332 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 1984 7.42 %
Rwork0.2146 24757 -
obs0.2165 26741 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.79 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 100 3458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01373448
X-RAY DIFFRACTIONf_angle_d1.1844682
X-RAY DIFFRACTIONf_chiral_restr0.0779510
X-RAY DIFFRACTIONf_plane_restr0.0067586
X-RAY DIFFRACTIONf_dihedral_angle_d20.18051278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.27061310.25641621X-RAY DIFFRACTION92.5
2.27-2.330.31511450.24031784X-RAY DIFFRACTION99.9
2.33-2.40.3171420.25621814X-RAY DIFFRACTION99.59
2.4-2.470.22511350.24471751X-RAY DIFFRACTION99.21
2.47-2.560.31331450.2381763X-RAY DIFFRACTION99.69
2.56-2.660.29521390.2421779X-RAY DIFFRACTION99.64
2.66-2.790.30491420.23391798X-RAY DIFFRACTION99.9
2.79-2.930.29451420.24671803X-RAY DIFFRACTION99.95
2.93-3.120.30411440.24831777X-RAY DIFFRACTION99.9
3.12-3.350.27981410.23991748X-RAY DIFFRACTION99.11
3.36-3.690.21011470.21751800X-RAY DIFFRACTION99.24
3.69-4.230.21211450.18971791X-RAY DIFFRACTION99.44
4.23-5.320.1841370.17681731X-RAY DIFFRACTION97.75
5.32-29.620.20981490.19811797X-RAY DIFFRACTION99.13

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