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- PDB-8agq: Crystal structure of anthocyanin-related GSTF8 from Populus trich... -

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Basic information

Entry
Database: PDB / ID: 8agq
TitleCrystal structure of anthocyanin-related GSTF8 from Populus trichocarpa in complex with (-)-catechin and glutathione
ComponentsGlutathione transferaseGlutathione S-transferase
KeywordsTRANSFERASE / Anthocyanin / Dehydratase
Function / homology
Function and homology information


glutathione binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / response to toxic substance / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
GLUTATHIONE / Chem-M5O / Glutathione transferase
Similarity search - Component
Biological speciesPopulus trichocarpa (black cottonwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.093 Å
AuthorsEichenberger, M. / Hueppi, S. / Schwander, T. / Mittl, P. / Buller, M.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation180544 Switzerland
CitationJournal: Nat Catal / Year: 2023
Title: The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis.
Authors: Eichenberger, M. / Schwander, T. / Huppi, S. / Kreuzer, J. / Mittl, P.R.E. / Peccati, F. / Jimenez-Oses, G. / Naesby, M. / Buller, R.M.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1718
Polymers24,4581
Non-polymers7137
Water5,621312
1
A: Glutathione transferase
hetero molecules

A: Glutathione transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,34116
Polymers48,9162
Non-polymers1,42514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5520 Å2
ΔGint-128 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.948, 55.447, 54.787
Angle α, β, γ (deg.)90.000, 113.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-680-

HOH

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Components

#1: Protein Glutathione transferase / Glutathione S-transferase


Mass: 24458.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus trichocarpa (black cottonwood) / Gene: POPTR_017G138800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9MWW0, glutathione transferase
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-M5O / (2~{S},3~{R})-2-[3,4-bis(oxidanyl)phenyl]-3,4-dihydro-2~{H}-chromene-3,5,7-triol / (-)-catechin


Mass: 290.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 1 part protein solution (30mM Tris pH 8, 200mM NaCl, 1mM EDTA) 1 part buffer (100mM MES pH 6.4, 200mM MgCl2, 17.9% PEG200)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.093→38.496 Å / Num. obs: 101092 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Net I/σ(I): 15.7
Reflection shellResolution: 1.093→1.11 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5007 / CC1/2: 0.817 / Rrim(I) all: 0.667

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F07

5f07


Resolution: 1.093→38.496 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.143 / WRfactor Rwork: 0.124 / SU B: 0.888 / SU ML: 0.018 / Average fsc free: 0.977 / Average fsc work: 0.9799 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1488 4917 4.881 %
Rwork0.1324 95821 -
all0.133 --
obs-100738 98.833 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.062 Å20 Å20.703 Å2
2---0.702 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.093→38.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 46 312 2076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122013
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161857
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.6412756
X-RAY DIFFRACTIONr_angle_other_deg0.6261.5714358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.5895.76913
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93710365
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.5251097
X-RAY DIFFRACTIONr_chiral_restr0.1030.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022384
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02400
X-RAY DIFFRACTIONr_nbd_refined0.2420.2447
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21641
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2956
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2956
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3770.223
X-RAY DIFFRACTIONr_nbd_other0.2320.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3310.251
X-RAY DIFFRACTIONr_mcbond_it2.8081.372962
X-RAY DIFFRACTIONr_mcbond_other2.80714.686962
X-RAY DIFFRACTIONr_mcangle_it3.5332.0651238
X-RAY DIFFRACTIONr_mcangle_other3.5322.1521239
X-RAY DIFFRACTIONr_scbond_it11.4451.7691051
X-RAY DIFFRACTIONr_scbond_other11.441052
X-RAY DIFFRACTIONr_scangle_it7.8082.4841517
X-RAY DIFFRACTIONr_scangle_other7.8052.4841518
X-RAY DIFFRACTIONr_lrange_it6.94324.5782504
X-RAY DIFFRACTIONr_lrange_other6.73120.5432391
X-RAY DIFFRACTIONr_rigid_bond_restr24.94132013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.093-1.1220.2313380.20970560.2175460.9630.97197.98570.193
1.122-1.1520.2463680.2469070.2473060.9450.94599.57570.228
1.152-1.1860.1663400.14567220.14670800.9820.98699.74580.125
1.186-1.2220.233260.19965410.269120.9620.96799.3490.184
1.222-1.2620.2073050.20863640.20867350.9530.96199.020.191
1.262-1.3060.2482950.25859630.25764210.9520.94897.46150.239
1.306-1.3560.1462740.11959910.1262930.9880.99199.55510.094
1.356-1.4110.1253260.09656900.09860170.990.99499.98340.079
1.411-1.4740.1553020.12555000.12758040.9840.99199.96550.106
1.474-1.5460.1242630.08952340.0955150.990.99599.67360.073
1.546-1.6290.1032460.07650150.07752640.9930.99799.9430.066
1.629-1.7280.1212310.07747300.07949650.9920.99699.91940.068
1.728-1.8470.122350.08744390.08946750.9910.99599.97860.08
1.847-1.9940.2071860.19741580.19843740.9710.96699.31410.171
1.994-2.1840.1162180.09837760.09940050.9920.99499.72530.098
2.184-2.4410.1341800.1130260.11136490.990.99387.85970.113
2.441-2.8160.1381720.11530640.11632400.9890.99299.87650.125
2.816-3.4450.1281310.12325930.12327320.9910.9999.70720.14
3.445-4.8520.1291050.11919020.11921310.9910.99294.18110.144
4.852-38.4960.144760.15811500.15712260.9890.9871000.197

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