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Yorodumi- PDB-2rcl: Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rcl | ||||||
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Title | Crystal Structure of Arabidopsis thaliana Allene Oxide Synthase (AOS, cytochrome P450 74A, CYP74A) Complexed with 12R,13S-Vernolic Acid at 2.4 A resolution | ||||||
Components | Cytochrome P450 74A | ||||||
Keywords | LYASE / P450 fold / Chloroplast / Fatty acid biosynthesis / Heme / Iron / Lipid synthesis / Metal-binding / Oxylipin biosynthesis / Transit peptide | ||||||
Function / homology | Function and homology information 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 | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.41 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 | 2rcl.cif.gz | 211 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rcl.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 2rcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rcl_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2rcl_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2rcl_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 2rcl_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/2rcl ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rcl | HTTPS FTP |
-Related structure data
Related structure data | 2rchC 2rcmC 3cliC 3dsiC 3dsjC 3dskC 2phq 2rcg 2rco 2rcp C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-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: CYP74A, AOS / Plasmid: pcWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q96242, hydroperoxide dehydratase #2: Chemical | #3: Chemical | ChemComp-T25 / ( | #4: Chemical | ChemComp-GOL / | #5: 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: 2.43 Å3/Da / Density % sol: 49.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG4000, 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: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 5, 2007 |
Radiation | Monochromator: double miror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. all: 42556 / Num. obs: 42556 / % possible obs: 99.8 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.5 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2PHQ 2phq Resolution: 2.41→88.39 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.586 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.231 / 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: 33.184 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→88.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.473 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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