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- PDB-7dw1: Crystal structure of a glutathione S-transferase SbGSTU6 from Sal... -

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Basic information

Entry
Database: PDB / ID: 7dw1
TitleCrystal structure of a glutathione S-transferase SbGSTU6 from Salix babylonica in complex with glutathione
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 / Glutathione S-transferase
Similarity search - Component
Biological speciesSalix babylonica (weeping willow)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 1.0Jul 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3244
Polymers52,7092
Non-polymers6152
Water1,18966
1
A: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6622
Polymers26,3551
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-4 kcal/mol
Surface area11240 Å2
MethodPISA
2
B: Glutathione S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6622
Polymers26,3551
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-3 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.013, 48.163, 83.990
Angle α, β, γ (deg.)90.000, 110.831, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-407-

HOH

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Components

#1: Protein Glutathione S-transferase


Mass: 26354.561 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: L-Proline, magnesium, HEFHS, 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: 2.27→30.9 Å / Num. obs: 17442 / % possible obs: 82.1 % / Redundancy: 6.56 % / Biso Wilson estimate: 28.77 Å2 / CC1/2: 1 / Net I/σ(I): 1.46
Reflection shellResolution: 2.27→2.59 Å / 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: 5KEJ

5kej


Resolution: 2.27→30.9 Å / SU ML: 0.3201 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 38.7374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3099 1699 9.74 %
Rwork0.2732 15743 -
obs0.2767 17442 82.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.29 Å2
Refinement stepCycle: LAST / Resolution: 2.27→30.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 40 66 3544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01573566
X-RAY DIFFRACTIONf_angle_d1.50114826
X-RAY DIFFRACTIONf_chiral_restr0.0997524
X-RAY DIFFRACTIONf_plane_restr0.0065614
X-RAY DIFFRACTIONf_dihedral_angle_d23.7541314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.340.47461190.44231033X-RAY DIFFRACTION66.09
2.34-2.420.43061220.41271125X-RAY DIFFRACTION70.17
2.42-2.50.40721210.38891175X-RAY DIFFRACTION74.06
2.5-2.60.42991300.37141217X-RAY DIFFRACTION77.95
2.6-2.720.40681360.35621205X-RAY DIFFRACTION75.72
2.72-2.870.38761360.32161234X-RAY DIFFRACTION77.8
2.87-3.050.32811470.31591370X-RAY DIFFRACTION85.85
3.05-3.280.33271440.2911421X-RAY DIFFRACTION88.77
3.28-3.610.27821570.26321433X-RAY DIFFRACTION90.14
3.61-4.130.24431490.23211408X-RAY DIFFRACTION87.92
4.13-5.20.25341680.20751543X-RAY DIFFRACTION95.8
5.2-30.90.26241700.2181579X-RAY DIFFRACTION94.29

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