+Open data
-Basic information
Entry | Database: PDB / ID: 6lsv | ||||||
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Title | Crystal structure of JOX2 in complex with 2OG, Fe, and JA | ||||||
Components | Probable 2-oxoglutarate-dependent dioxygenase At5g05600 | ||||||
Keywords | PLANT PROTEIN / jasmonic acid / 2OG oxygenase | ||||||
Function / homology | Function and homology information jasmonic acid hydrolase / response to karrikin / regulation of jasmonic acid mediated signaling pathway / flavonoid biosynthetic process / cellular response to toxic substance / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å | ||||||
Authors | Zhang, X. / Wang, D. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Mol Plant / Year: 2021 Title: Structure-guided analysis of Arabidopsis JASMONATE-INDUCED OXYGENASE (JOX) 2 reveals key residues for recognition of jasmonic acid substrate by plant JOXs. Authors: Zhang, X. / Wang, D. / Elberse, J. / Qi, L. / Shi, W. / Peng, Y.L. / Schuurink, R.C. / Van den Ackerveken, G. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lsv.cif.gz | 151.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lsv.ent.gz | 116.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/6lsv ftp://data.pdbj.org/pub/pdb/validation_reports/ls/6lsv | HTTPS FTP |
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-Related structure data
Related structure data | 1gp4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40121.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g05600, MOP10.14 / Production host: Escherichia coli (E. coli) References: UniProt: Q9FFF6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, pH 7.5, 1.26M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. obs: 23124 / % possible obs: 98.96 % / Redundancy: 6.8 % / CC1/2: 0.988 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.054 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.64→2.69 Å / Redundancy: 7 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 2225 / CC1/2: 0.934 / Rpim(I) all: 0.193 / % possible all: 96.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GP4 Resolution: 2.651→26.334 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.21 / 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: 99.81 Å2 / Biso mean: 33.0983 Å2 / Biso min: 15.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.651→26.334 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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