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- PDB-5a4v: AtGSTF2 from Arabidopsis thaliana in complex with quercetin -

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Basic information

Entry
Database: PDB / ID: 5a4v
TitleAtGSTF2 from Arabidopsis thaliana in complex with quercetin
ComponentsGLUTATHIONE S-TRANSFERASE F2
KeywordsTRANSFERASE / GLUTATHIONE-S-TRANSFERASE / GST / PLANT / ARABIDOPSIS
Function / homology
Function and homology information


response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / auxin-activated signaling pathway / glutathione binding / apoplast / plasmodesma / plant-type vacuole ...response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / auxin-activated signaling pathway / glutathione binding / apoplast / plasmodesma / plant-type vacuole / chloroplast stroma / response to zinc ion / glutathione transferase / glutathione transferase activity / response to cadmium ion / response to cold / chloroplast / peroxidase activity / defense response / protein domain specific binding / intracellular membrane-bounded organelle / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
Glutathione S-transferases Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 Phi, C-terminal / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / 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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / Glutathione S-transferase F2
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsAhmad, L. / Rylott, E. / Bruce, N.C. / Edwards, R. / Grogan, G.
CitationJournal: FEBS Open Bio / Year: 2017
Title: Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands.
Authors: Ahmad, L. / Rylott, E.L. / Bruce, N.C. / Edwards, R. / Grogan, G.
History
DepositionJun 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references / Structure summary
Revision 1.2Mar 1, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE F2
B: GLUTATHIONE S-TRANSFERASE F2
C: GLUTATHIONE S-TRANSFERASE F2
D: GLUTATHIONE S-TRANSFERASE F2
E: GLUTATHIONE S-TRANSFERASE F2
F: GLUTATHIONE S-TRANSFERASE F2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,23615
Polymers144,9756
Non-polymers1,2619
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15320 Å2
ΔGint-131 kcal/mol
Surface area48530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.030, 94.830, 153.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.686, 0.07327, -0.7239), (0.07484, -0.9825, -0.1704), (-0.7237, -0.1711, 0.6686)-34.29, -4.816, -15.45
2given(-0.2097, -0.213, -0.9543), (-0.3025, 0.9422, -0.1438), (0.9298, 0.2585, -0.2621)-34.29, -4.816, -15.45
3given(-0.5545, 0.01725, 0.832), (0.1438, -0.9828, 0.1162), (0.8197, 0.184, 0.5424)2.414, 5.258, -2.296
4given(0.9917, 0.1097, -0.06678), (0.1095, -0.994, -0.006776), (-0.06712, -0.000591, -0.9977)1.067, 2.844, -54
5given(-0.6279, -0.151, 0.7635), (-0.03881, 0.9858, 0.1631), (-0.7774, 0.07278, -0.6248)4.334, 1.999, -52.82

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE F2 / ATGSTF2 / 24 KDA AUXIN-BINDING PROTEIN / ATPM24 / GST CLASS-PHI MEMBER 2 / ATGSTF2


Mass: 24162.566 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): TUNER / References: UniProt: P46422, glutathione transferase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H10O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M PTCP (PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE SYSTEM), 15% PEG 1.5K, PROTEIN AT 10 MG PER ML, pH 7

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.38→59.09 Å / Num. obs: 52158 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shellResolution: 2.38→2.44 Å / Redundancy: 7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GNW

1gnw


Resolution: 2.38→59.59 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.227 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.547 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24472 2506 4.8 %RANDOM
Rwork0.20286 ---
obs0.20483 49588 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.484 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å20 Å2
2--4.95 Å20 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.38→59.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9868 0 90 326 10284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01910221
X-RAY DIFFRACTIONr_bond_other_d0.0090.029570
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.95613891
X-RAY DIFFRACTIONr_angle_other_deg1.645321914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48551259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79424.256484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.761151640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3131553
X-RAY DIFFRACTIONr_chiral_restr0.0980.21565
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211622
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022389
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.643.4895039
X-RAY DIFFRACTIONr_mcbond_other2.6373.4895032
X-RAY DIFFRACTIONr_mcangle_it3.915.2236281
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0153.7625182
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 195 -
Rwork0.266 3636 -
obs--99.92 %

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