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- PDB-5eco: Crystal Structure of FIN219-FIP1 complex with JA, Leu and Mg -

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Basic information

Entry
Database: PDB / ID: 5eco
TitleCrystal Structure of FIN219-FIP1 complex with JA, Leu and Mg
Components
  • Glutathione S-transferase U20
  • Jasmonic acid-amido synthetase JAR1
KeywordsLIGASE/TRANSFERASE / Jasmonate-amido synthetase / Glutathione S-transferase / Ligase-Transferase complex
Function / homology
Function and homology information


jasmonoyl-L-amino acid ligase / jasmonoyl-L-amino acid ligase activity / regulation of response to red or far red light / cellular response to auxin stimulus / induced systemic resistance, jasmonic acid mediated signaling pathway / L-leucine binding / toxin catabolic process / acid-amino acid ligase activity / protein adenylylation / response to mycotoxin ...jasmonoyl-L-amino acid ligase / jasmonoyl-L-amino acid ligase activity / regulation of response to red or far red light / cellular response to auxin stimulus / induced systemic resistance, jasmonic acid mediated signaling pathway / L-leucine binding / toxin catabolic process / acid-amino acid ligase activity / protein adenylylation / response to mycotoxin / response to gravity / glutathione binding / apoplast / response to UV-B / amino acid binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chloroplast / enzyme binding / mitochondrion / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
GH3 family / GH3 family N-terminal domain / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like ...GH3 family / GH3 family N-terminal domain / 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 Yfyf (Class Pi); Chain A, domain 2 - #10 / 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
GLUTATHIONE / Chem-JAA / LEUCINE / Glutathione S-transferase U20 / Jasmonoyl--L-amino acid synthetase JAR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChen, C.Y. / Cheng, Y.S.
Citation
Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of jasmonate-amido synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation
Authors: Chen, C.Y. / Ho, S.S. / Kuo, T.Y. / Hsieh, H.L. / Cheng, Y.S.
#1: Journal: Science / Year: 2012
Title: Structural basis for prereceptor modulation of plant hormones by GH3 proteins.
Authors: Westfall, C.S. / Zubieta, C. / Herrmann, J. / Kapp, U. / Nanao, M.H. / Jez, J.M.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Jasmonic acid-amido synthetase JAR1
B: Glutathione S-transferase U20
C: Glutathione S-transferase U20
D: Jasmonic acid-amido synthetase JAR1
E: Glutathione S-transferase U20
F: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,23815
Polymers232,3026
Non-polymers1,9369
Water41,5792308
1
A: Jasmonic acid-amido synthetase JAR1
B: Glutathione S-transferase U20
C: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1318
Polymers116,1513
Non-polymers9805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Jasmonic acid-amido synthetase JAR1
E: Glutathione S-transferase U20
F: Glutathione S-transferase U20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1077
Polymers116,1513
Non-polymers9564
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.759, 53.836, 192.574
Angle α, β, γ (deg.)90.070, 89.960, 113.530
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 6 molecules ADBCEF

#1: Protein Jasmonic acid-amido synthetase JAR1 / Jasmonate-amino acid synthetase JAR1 / Protein FAR-RED INSENSITIVE 219 / Protein JASMONATE RESISTANT 1


Mass: 64416.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: JAR1, FIN219, At2g46370, F11C10.6 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9SKE2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein
Glutathione S-transferase U20 / AtGSTU20 / FIN219-interacting protein 1 / GST class-tau member 20


Mass: 25867.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GSTU20, FIP1, At1g78370, F3F9.11 / Plasmid: pRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8L7C9, glutathione transferase

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Non-polymers , 5 types, 2317 molecules

#3: Chemical ChemComp-JAA / {(1R,2R)-3-oxo-2-[(2Z)-pent-2-en-1-yl]cyclopentyl}acetic acid


Mass: 210.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O3 / Comment: hormone*YM
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N3O6S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2308 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, 30%(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762-0.97622
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 8, 2012
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.976221
ReflectionResolution: 1.8→50 Å / Num. obs: 174895 / % possible obs: 94.9 % / Redundancy: 1.8 % / Biso Wilson estimate: 8.57 Å2 / Rmerge(I) obs: 0.066 / Χ2: 0.996 / Net I/av σ(I): 8.962 / Net I/σ(I): 6.9 / Num. measured all: 316315
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 % / Rejects: _

Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.860.443174821.00695.9
1.86-1.940.313175550.99896
1.94-2.030.232177530.99796.3
2.03-2.130.176175830.98396.2
2.13-2.270.128176421.0296
2.27-2.440.099175521.00295.5
2.44-2.690.08173600.99194.7
2.69-3.080.061170520.97193.5
3.08-3.880.047167451.00891.5
3.88-500.045170820.97993.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v708data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX1.9_1692+svnmodel building
Coot0.8.2model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EPL

4epl


Resolution: 1.8→23.483 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 17478 9.99 %
Rwork0.222 157417 -
obs0.2236 174895 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 36.2 Å2 / Biso mean: 6.8841 Å2 / Biso min: 2 Å2
Refinement stepCycle: final / Resolution: 1.8→23.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15950 0 129 2309 18388
Biso mean--8.48 4.69 -
Num. residues----1994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916480
X-RAY DIFFRACTIONf_angle_d1.7822304
X-RAY DIFFRACTIONf_chiral_restr0.0872386
X-RAY DIFFRACTIONf_plane_restr0.0112892
X-RAY DIFFRACTIONf_dihedral_angle_d16.8856100
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82050.18395330.17944713524688
1.8205-1.84190.18236120.17875433604597
1.8419-1.86430.19125950.18265206580196
1.8643-1.88790.20035740.17165229580396
1.8879-1.91280.18995950.17115447604297
1.9128-1.93890.19565860.17775213579997
1.9389-1.96660.20275800.18185332591296
1.9666-1.9960.18835980.17675383598197
1.996-2.02710.18725880.1745304589297
2.0271-2.06040.18245880.16955402599097
2.0604-2.09590.19215830.17425245582897
2.0959-2.1340.20715840.18685279586397
2.134-2.1750.20996010.20335408600997
2.175-2.21930.20825720.19935257582996
2.2193-2.26760.20526020.19285363596596
2.2676-2.32030.21795830.19435240582396
2.3203-2.37820.25055910.2395263585496
2.3782-2.44250.25336010.23425429603096
2.4425-2.51430.24015680.2075155572396
2.5143-2.59530.22285870.22165288587596
2.5953-2.68790.22925970.22095318591595
2.6879-2.79540.26755730.22865113568695
2.7954-2.92240.24115830.2275172575594
2.9224-3.07620.26535730.24255210578395
3.0762-3.26840.26915720.24315160573294
3.2684-3.520.28515790.25785160573994
3.52-3.87280.26035670.24825089565692
3.8728-4.430.22745600.2395047560792
4.43-5.5690.29255560.2655189574594
5.569-23.48510.36995970.32085370596797

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