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- PDB-5gzz: Crystal Structure of FIN219-SjGST complex with JA -

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Basic information

Entry
Database: PDB / ID: 5gzz
TitleCrystal Structure of FIN219-SjGST complex with JA
Components
  • Glutathione S-transferase class-mu 26 kDa isozyme
  • 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 / protein adenylylation / response to mycotoxin / response to UV-B / amino acid 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 / L-leucine binding / protein adenylylation / response to mycotoxin / response to UV-B / amino acid binding / glutathione transferase / glutathione transferase activity / glutathione metabolic process / enzyme binding / ATP binding / cytoplasm
Similarity search - Function
: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family ...: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / 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 / Glutathione S-transferase class-mu 26 kDa isozyme / Jasmonoyl--L-amino acid synthetase JAR1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Schistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.386 Å
AuthorsChen, C.Y. / Cheng, Y.S.
CitationJournal: 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.
History
DepositionOct 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: 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 class-mu 26 kDa isozyme
C: Glutathione S-transferase class-mu 26 kDa isozyme
D: Glutathione S-transferase class-mu 26 kDa isozyme
E: Glutathione S-transferase class-mu 26 kDa isozyme
F: Glutathione S-transferase class-mu 26 kDa isozyme
G: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,67914
Polymers217,6257
Non-polymers2,0547
Water17,312961
1
A: Jasmonic acid-amido synthetase JAR1
B: Glutathione S-transferase class-mu 26 kDa isozyme
C: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3116
Polymers115,4863
Non-polymers8253
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glutathione S-transferase class-mu 26 kDa isozyme
E: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6844
Polymers51,0692
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Glutathione S-transferase class-mu 26 kDa isozyme
G: Glutathione S-transferase class-mu 26 kDa isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6844
Polymers51,0692
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.274, 91.802, 91.728
Angle α, β, γ (deg.)89.990, 89.990, 89.930
Int Tables number1
Space group name H-MP1
DetailsChain D-G are the molecular packing in the protein crystal and not included in the unit of biological assembly

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Components

#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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: JAR1, FIN219, AtGH3.11 / 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 class-mu 26 kDa isozyme / Glutathione S-transferase SjGST / GST 26 / Sj26 antigen / SjGST


Mass: 25534.723 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Gene: SjGST / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08515, glutathione transferase
#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.: 1 / Source method: obtained synthetically / Formula: C12H18O3 / Comment: hormone*YM
#4: Chemical
ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.24 Å3/Da / Density % sol: 45.03 % / Mosaicity: 1.227 ° / Mosaicity esd: 0.012 °
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 8.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris-HCl, 40%(w/v) PEG 4000

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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: Mar 30, 2012
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
20.976221
ReflectionResolution: 2.4→50 Å / Num. obs: 73703 / % possible obs: 97.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 13.22 Å2 / Rmerge(I) obs: 0.05 / Χ2: 1.006 / Net I/av σ(I): 15.426 / Net I/σ(I): 10.1 / Num. measured all: 141298
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.491.90.43972861.00797.5
2.49-2.591.90.347236197.2
2.59-2.71.90.25472201.00897.7
2.7-2.851.90.18873180.99697.8
2.85-3.021.90.13373051.01197.8
3.02-3.2620.0867230197.9
3.26-3.5820.05573010.97697.8
3.58-4.120.03572480.98697.4
4.1-5.1720.02572741.0297.5
5.17-5020.02871411.05796

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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: 2.386→26.209 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 19.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 7454 10.11 %
Rwork0.2037 66249 -
obs0.2067 73703 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.11 Å2 / Biso mean: 15.9573 Å2 / Biso min: 2 Å2
Refinement stepCycle: final / Resolution: 2.386→26.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15147 0 135 961 16243
Biso mean--8.49 13.31 -
Num. residues----1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815667
X-RAY DIFFRACTIONf_angle_d1.48121166
X-RAY DIFFRACTIONf_chiral_restr0.0592255
X-RAY DIFFRACTIONf_plane_restr0.0082700
X-RAY DIFFRACTIONf_dihedral_angle_d16.7165888
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 (%)
2.3855-2.41260.20312120.1761997220987
2.4126-2.4410.24962590.186421932452100
2.441-2.47070.2232630.180322302493100
2.4707-2.5020.21092500.176322792529100
2.502-2.53490.22452540.18421982452100
2.5349-2.56960.19772640.173122032467100
2.5696-2.60620.19962420.174522062448100
2.6062-2.64510.19792500.173522052455100
2.6451-2.68640.21312460.18522382484100
2.6864-2.73040.18232600.18322652525100
2.7304-2.77740.20532550.173322092464100
2.7774-2.82790.21882510.187622122463100
2.8279-2.88220.20222460.178622352481100
2.8822-2.9410.20392490.191722272476100
2.941-3.00480.1912430.175522882531100
3.0048-3.07460.23672390.192321752414100
3.0746-3.15140.20882760.175622552531100
3.1514-3.23640.22352360.207721452381100
3.2364-3.33150.22312450.18982241248699
3.3315-3.43880.21352530.179921892442100
3.4388-3.56140.232600.20182253251399
3.5614-3.70360.23322340.20292192242699
3.7036-3.87170.23782610.19752224248599
3.8717-4.07510.23792330.19732211244499
4.0751-4.32940.24352550.20472251250699
4.3294-4.66190.26792510.22662142239399
4.6619-5.12790.27042460.24432235248199
5.1279-5.86270.22622370.23272189242699
5.8627-7.35910.28992440.255522322476100
7.3591-26.21060.33982400.29372130237095

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