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Open data
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Basic information
Entry | Database: PDB / ID: 5eci | ||||||
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Title | Crystal Structure of FIN219-FIP1 complex with JA, ATP and Mg | ||||||
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![]() | LIGASE/TRANSFERASE / Jasmonate-amido synthetase / Glutathione S-transferase / Ligase-Transferase complex | ||||||
Function / homology | ![]() 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 / acid-amino acid ligase activity / response to mycotoxin / protein adenylylation ...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 / acid-amino acid ligase activity / response to mycotoxin / protein adenylylation / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, C.Y. / Cheng, Y.S. | ||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 437 KB | Display | ![]() |
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PDB format | ![]() | 340.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 114.2 KB | Display | |
Data in CIF | ![]() | 165.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5echC ![]() 5eckC ![]() 5eclC ![]() 5ecmC ![]() 5ecnC ![]() 5ecoC ![]() 5ecpC ![]() 5ecqC ![]() 5ecrC ![]() 5ecsC ![]() 5gzzC ![]() 4eplS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 6 molecules ADBCEF
#1: Protein | Mass: 64416.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9SKE2, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein | Mass: 25867.312 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1816 molecules ![](data/chem/img/JAA.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GSH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GSH.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GSH / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.77 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 8, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.56→50 Å / Num. obs: 275166 / % possible obs: 96.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 2.02 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.01 / Net I/av σ(I): 13.508 / Net I/σ(I): 6.7 / Num. measured all: 1043208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EPL Resolution: 1.56→24.568 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 18.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 34.93 Å2 / Biso mean: 3.2918 Å2 / Biso min: 2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→24.568 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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