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- PDB-3dsj: Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase V... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dsj | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase Variant (F137L) (At-AOS(F137L), cytochrome P450 74A, CYP74A) Complexed with 13(S)-HOD at 1.60 A Resolution | ||||||
![]() | Cytochrome P450 74A, chloroplast | ||||||
![]() | LYASE / P450 fold / Chloroplast / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / Metal-binding / Oxylipin biosynthesis / Transit peptide | ||||||
Function / homology | ![]() oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / jasmonic acid biosynthetic process / response to jasmonic acid / oxylipin biosynthetic process / epoxygenase P450 pathway / chloroplast thylakoid / response to fungus / plastoglobule ...oxylipin metabolic process / hydroperoxide dehydratase / allene oxide synthase activity / jasmonic acid biosynthetic process / response to jasmonic acid / oxylipin biosynthetic process / epoxygenase P450 pathway / chloroplast thylakoid / response to fungus / plastoglobule / sterol metabolic process / thylakoid / chloroplast envelope / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / plastid / chloroplast thylakoid membrane / defense response to fungus / monooxygenase activity / chloroplast / defense response / oxygen binding / response to wounding / iron ion binding / heme binding / mitochondrion Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, D.S. / Nioche, P. / Raman, C.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.7 KB | Display | ![]() |
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PDB format | ![]() | 172.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 43.9 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rchC ![]() 2rclC ![]() 2rcmC ![]() 3cliSC ![]() 3dsiC ![]() 3dskC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 55732.570 Da / Num. of mol.: 2 / Fragment: UNP residues 34-518 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 824 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/243.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/243.gif)
![](data/chem/img/OCT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-243 / ( | #4: Chemical | ChemComp-OCT / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG4000, Glycerol, Tris-HCL, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2007 |
Radiation | Monochromator: double miror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. all: 143685 / Num. obs: 143685 / % possible obs: 99.7 % |
Reflection shell | Resolution: 1.6→1.64 Å / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CLI Resolution: 1.6→88.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.454 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.037 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→88.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.597→1.638 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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