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- PDB-7dw2: Crystal structure of a glutathione S-transferase SbGSTU6 from Sal... -

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Basic information

Entry
Database: PDB / ID: 7dw2
TitleCrystal structure of a glutathione S-transferase SbGSTU6 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 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: 1.74 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
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
B: Glutathione S-transferase
C: Glutathione S-transferase
D: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)105,4184
Polymers105,4184
Non-polymers00
Water12,520695
1
A: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)26,3551
Polymers26,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)26,3551
Polymers26,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)26,3551
Polymers26,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutathione S-transferase


Theoretical massNumber of molelcules
Total (without water)26,3551
Polymers26,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.146, 103.146, 186.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Glutathione S-transferase


Mass: 26354.561 Da / Num. of mol.: 4
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


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: L-Proline, magnesium acetate tetrahydrate, HEPES, sodium cacodylate trihydrate

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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: 1.74→42.42 Å / Num. obs: 104707 / % possible obs: 95.8 % / Redundancy: 1 % / Biso Wilson estimate: 26.03 Å2 / CC1/2: 1 / Net I/σ(I): 1.65
Reflection shellResolution: 1.74→1.97 Å / Num. unique obs: 10155 / 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: 7DW1

7dw1


Resolution: 1.74→31.03 Å / SU ML: 0.2033 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.8293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 1932 1.91 %
Rwork0.1925 99137 -
obs0.1932 101069 95.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.19 Å2
Refinement stepCycle: LAST / Resolution: 1.74→31.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6936 0 0 695 7631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00967116
X-RAY DIFFRACTIONf_angle_d1.06469632
X-RAY DIFFRACTIONf_chiral_restr0.07281048
X-RAY DIFFRACTIONf_plane_restr0.00681220
X-RAY DIFFRACTIONf_dihedral_angle_d20.89712640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.29931170.27796196X-RAY DIFFRACTION84.76
1.79-1.830.3351240.25646421X-RAY DIFFRACTION87.75
1.83-1.890.26671320.2386604X-RAY DIFFRACTION90.97
1.89-1.950.28211330.22136958X-RAY DIFFRACTION95.13
1.95-2.020.23791370.21317038X-RAY DIFFRACTION96.31
2.02-2.10.30741400.20427087X-RAY DIFFRACTION96.92
2.1-2.190.20631400.20167149X-RAY DIFFRACTION96.9
2.19-2.310.23731420.19137262X-RAY DIFFRACTION98.65
2.31-2.460.21631410.19587242X-RAY DIFFRACTION98.94
2.46-2.640.21681440.19847354X-RAY DIFFRACTION98.98
2.64-2.910.22381430.19867254X-RAY DIFFRACTION98.31
2.91-3.330.23791450.19537458X-RAY DIFFRACTION99.75
3.33-4.20.17991440.1697391X-RAY DIFFRACTION98.79
4.2-31.030.23441500.17997723X-RAY DIFFRACTION98.75

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