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- PDB-5a4u: AtGSTF2 from Arabidopsis thaliana in complex with indole-3-aldehyde -

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Basic information

Entry
Database: PDB / ID: 5a4u
TitleAtGSTF2 from Arabidopsis thaliana in complex with indole-3-aldehyde
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 / glutathione binding / apoplast / auxin-activated signaling pathway / plant-type vacuole / plasmodesma ...response to oomycetes / camalexin binding / quercitrin binding / salicylic acid binding / toxin catabolic process / glutathione binding / apoplast / auxin-activated signaling pathway / plant-type vacuole / plasmodesma / 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 / 1H-INDOLE-3-CARBALDEHYDE / Glutathione S-transferase F2
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)146,43219
Polymers144,9756
Non-polymers1,45613
Water7,278404
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16620 Å2
ΔGint-47.9 kcal/mol
Surface area47480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.860, 94.410, 152.380
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(-0.6935, 0.06444, -0.7176), (0.07266, -0.9847, -0.1586), (-0.7168, -0.1622, 0.6781)-33.99, -3.899, -14.87
2given(-0.2047, -0.233, -0.9507), (-0.291, 0.9418, -0.1682), (0.9346, 0.2422, -0.2606)-33.8, -8.578, -18.79
3given(-0.5467, 0.04874, 0.8359), (0.137, -0.9796, 0.1467), (0.8261, 0.1947, 0.5289)2.558, 6.188, -2.259
4given(0.9887, 0.1358, -0.06403), (0.1356, -0.9907, -0.007312), (-0.06443, -0.001453, -0.9979)1.076, 3.269, -53.77
5given(-0.6318, -0.1686, 0.7566), (-0.5692, 0.9835, 0.1716), (-0.7731, 0.06535, -0.6309)4.198, 1.661, -52.74

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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-I3A / 1H-INDOLE-3-CARBALDEHYDE


Mass: 145.158 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H7NO
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 0.1M PCTP (PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE SYSTEM, 15% (W/V) PEG 1.5K PH 7.0. PROTEIN AT 10 MG PER ML

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→94.41 Å / Num. obs: 86285 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 8 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.3 / % 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→80.38 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.839 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23353 4311 5 %RANDOM
Rwork0.19757 ---
obs0.19935 81894 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--3.38 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2→80.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9897 0 108 404 10409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910265
X-RAY DIFFRACTIONr_bond_other_d0.0120.029658
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.95813934
X-RAY DIFFRACTIONr_angle_other_deg1.9193.00122116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35851261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29824.295482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.894151660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1111552
X-RAY DIFFRACTIONr_chiral_restr0.1070.21567
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211654
X-RAY DIFFRACTIONr_gen_planes_other0.010.022428
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_it2.9613.1635049
X-RAY DIFFRACTIONr_mcbond_other2.963.1635043
X-RAY DIFFRACTIONr_mcangle_it3.9244.7336296
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.713.4725216
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 326 -
Rwork0.269 5976 -
obs--99.98 %

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