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- PDB-5ecp: Crystal Structure of FIN219-FIP1 complex with JA, MET and ATP -

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Basic information

Entry
Database: PDB / ID: 5ecp
TitleCrystal Structure of FIN219-FIP1 complex with JA, MET and ATP
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 / toxin catabolic process / L-leucine binding / protein adenylylation / response to mycotoxin / glutathione binding ...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 / toxin catabolic process / L-leucine binding / protein adenylylation / response to mycotoxin / glutathione binding / apoplast / response to UV-B / amino acid binding / response to gravity / glutathione transferase / glutathione transferase activity / glutathione metabolic process / chloroplast / enzyme binding / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / GH3 family central domain / GH3 family C-terminal domain / 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 ...: / : / GH3 family central domain / GH3 family C-terminal domain / 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
ADENOSINE-5'-TRIPHOSPHATE / GLUTATHIONE / Chem-JAA / METHIONINE / 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: 2.25001563827 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)235,26416
Polymers232,3026
Non-polymers2,96310
Water28,2301567
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)117,6328
Polymers116,1513
Non-polymers1,4815
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)117,6328
Polymers116,1513
Non-polymers1,4815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.708, 53.701, 192.029
Angle α, β, γ (deg.)89.960, 90.160, 113.240
Int Tables number1
Space group name H-MP1
Space group name HallP1

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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, 1577 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
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#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.: 1567 / 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: 2.25 Å3/Da / Density % sol: 45.31 %
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: 0.97620-0.97622
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: 2.25→50 Å / Num. obs: 89193 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 11.4260880168 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/av σ(I): 4.936 / Net I/σ(I): 4.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.992 / Rsym value: 0.406 / % possible all: 96.7

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Processing

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

4epl


Resolution: 2.25001563827→23.3466904213 Å / SU ML: 0.192312522226 / Cross valid method: FREE R-VALUE / σ(F): 1.5464298217 / Phase error: 15.6550644699
RfactorNum. reflection% reflection
Rfree0.207669625333 2253 2.52598298073 %
Rwork0.184636263104 86940 -
obs0.185207158756 89193 95.4681194944 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.4892268594 Å2
Refinement stepCycle: final / Resolution: 2.25001563827→23.3466904213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15950 0 190 1567 17707
Biso mean--17.3 11.44 -
Num. residues----1994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015310771607816546
X-RAY DIFFRACTIONf_angle_d1.6390064815422406
X-RAY DIFFRACTIONf_chiral_restr0.06681406369652392
X-RAY DIFFRACTIONf_plane_restr0.008167287068062894
X-RAY DIFFRACTIONf_dihedral_angle_d19.36563168426034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.29890.1532659893971390.1347700722425315X-RAY DIFFRACTION94.1156169111
2.2989-2.35230.1304819964361440.1143049845645681X-RAY DIFFRACTION99.3349249659
2.3523-2.41110.1290851996471520.1125234586015606X-RAY DIFFRACTION99.4473229706
2.4111-2.47620.1344499816681420.1182484984955667X-RAY DIFFRACTION99.3331053352
2.4762-2.5490.1600492940111530.1320192864815701X-RAY DIFFRACTION98.718381113
2.549-2.63120.1207146333381430.1158709237645490X-RAY DIFFRACTION98.479020979
2.6312-2.72510.1563311680961450.133840852075615X-RAY DIFFRACTION98.5120574654
2.7251-2.8340.178192719791510.1420243650655713X-RAY DIFFRACTION98.6541049798
2.834-2.96270.201995966121370.1517462806525528X-RAY DIFFRACTION97.2031571723
2.9627-3.11860.1832369631911450.1533580950445388X-RAY DIFFRACTION95.2487519367
3.1186-3.31350.2167260676781420.1698965704545367X-RAY DIFFRACTION93.9300937766
3.3135-3.56850.2028281445441370.1755671936465245X-RAY DIFFRACTION92.1417565485
3.5685-3.92610.24297444711260.212748817915125X-RAY DIFFRACTION90.1923737547
3.9261-4.49070.2506495348251360.2418471988895186X-RAY DIFFRACTION90.2952154734
4.4907-5.64450.2903629955771240.2849008274165121X-RAY DIFFRACTION90.9327323162
5.6445-23.34790.3881362636581370.3326574704235192X-RAY DIFFRACTION90.9230506739

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