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- PDB-8jzk: Crystal structure of glutathione S-transferase Tau7 from Salix li... -

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Basic information

Entry
Database: PDB / ID: 8jzk
TitleCrystal structure of glutathione S-transferase Tau7 from Salix lindleyana in complex with GSH
Componentsglutathione transferase
KeywordsTRANSFERASE / glutathione $-transferase / Tau class / GSH
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity / glutathione metabolic process / cytoplasm
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 / 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-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 / 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 transferase
Similarity search - Component
Biological speciesSalix lindleyana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55004430946 Å
AuthorsXu, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of glutathione S-transferase Tau7 from Salix lindleyana in complex with GSH
Authors: Xu, N.
History
DepositionJul 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0632
Polymers25,7561
Non-polymers3071
Water68538
1
A: glutathione transferase
hetero molecules

A: glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1264
Polymers51,5122
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.727, 87.931, 113.973
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein glutathione transferase


Mass: 25755.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Salix lindleyana is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A5N5L538.
Source: (gene. exp.) Salix lindleyana (plant) / Gene: DKX38_015263
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A5N5L538
#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.: 38 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS propane pH 9.0, 8% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.55004430946→29.3401515991 Å / Num. obs: 10186 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 25.969849838 Å2 / CC1/2: 0.978 / Rpim(I) all: 0.071 / Rrim(I) all: 0.233 / Net I/σ(I): 9.7
Reflection shellResolution: 2.55004430946→2.55004430946 Å / Num. unique obs: 724 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55004430946→29.3401515991 Å / SU ML: 0.301574382114 / Cross valid method: FREE R-VALUE / σ(F): 1.38496459539 / Phase error: 23.8417971238
RfactorNum. reflection% reflection
Rfree0.258354324323 491 4.8241304775 %
Rwork0.188358358396 9687 -
obs0.19172701895 10178 99.1814461119 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.5274376791 Å2
Refinement stepCycle: LAST / Resolution: 2.55004430946→29.3401515991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 20 38 1825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008895335870191839
X-RAY DIFFRACTIONf_angle_d1.146029649212488
X-RAY DIFFRACTIONf_chiral_restr0.0469363057102260
X-RAY DIFFRACTIONf_plane_restr0.00551251287418317
X-RAY DIFFRACTIONf_dihedral_angle_d16.532167743688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.80650.2899916701791200.2068888326822374X-RAY DIFFRACTION98.7722772277
2.8065-3.21220.292859313931290.2160556832082358X-RAY DIFFRACTION99.0442054958
3.2122-4.04530.2784249192631100.1806597297992440X-RAY DIFFRACTION99.3377483444
4.0453-29.34210.2134942395261320.1734898914062515X-RAY DIFFRACTION99.5487025197

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