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Yorodumi- PDB-3cli: Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cli | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase (AOS, cytochrome P450 74A, CYP74A) at 1.80 A Resolution | ||||||
Components | Allene Oxide Synthase | ||||||
Keywords | LYASE / P450 fold | ||||||
Function / homology | Function and homology information oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / jasmonic acid biosynthetic process / epoxygenase P450 pathway / response to jasmonic acid / oxylipin biosynthetic process / chloroplast thylakoid / plastoglobule / response to fungus ...oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / jasmonic acid biosynthetic process / epoxygenase P450 pathway / response to jasmonic acid / oxylipin biosynthetic process / chloroplast thylakoid / plastoglobule / response to fungus / thylakoid / sterol metabolic process / chloroplast envelope / plastid / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / chloroplast thylakoid membrane / defense response to fungus / chloroplast / monooxygenase activity / defense response / oxygen binding / response to wounding / iron ion binding / heme binding / mitochondrion Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Lee, D.-S. / Nioche, P. / Raman, C.S. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes Authors: Lee, D.-S. / Nioche, P. / Hamberg, M. / Raman, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cli.cif.gz | 213.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cli.ent.gz | 168.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cl/3cli ftp://data.pdbj.org/pub/pdb/validation_reports/cl/3cli | HTTPS FTP |
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-Related structure data
Related structure data | 2rchC 2rclC 2rcmC 3dsiC 3dsjC 3dskC C: citing same article (ref.) |
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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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Details | the biological assembly is a monomer |
-Components
#1: Protein | Mass: 55766.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AOS, CYP74A / Plasmid: pcWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q96242, hydroperoxide dehydratase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000, Glycerol, Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2007 |
Radiation | Monochromator: double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 100757 / Num. obs: 100757 / % possible obs: 99.2 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.84 Å / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→88.39 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.194 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→88.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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