+Open data
-Basic information
Entry | Database: PDB / ID: 2r6j | ||||||
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Title | Structure of Eugenol Synthase from Ocimum basilicum | ||||||
Components | Eugenol synthase 1 | ||||||
Keywords | PLANT PROTEIN / eugenol / phenylpropene / PIP reductase / short-chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information eugenol synthase / eugenol biosynthetic process / oxidoreductase activity / nucleotide binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Ocimum basilicum (sweet basil) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Louie, G.V. / Noel, J.P. / Bowman, M.E. | ||||||
Citation | Journal: Plos One / Year: 2007 Title: Structure and reaction mechanism of basil eugenol synthase Authors: Louie, G.V. / Baiga, T.J. / Bowman, M.E. / Koeduka, T. / Taylor, J.H. / Spassova, S.M. / Pichersky, E. / Noel, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r6j.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r6j.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 2r6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r6j_validation.pdf.gz | 975.2 KB | Display | wwPDB validaton report |
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Full document | 2r6j_full_validation.pdf.gz | 985.3 KB | Display | |
Data in XML | 2r6j_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 2r6j_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/2r6j ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r6j | HTTPS FTP |
-Related structure data
Related structure data | 2qw8SC 2qx7C 2qysC 2qzzC 2r2gC S: Starting model for refinement 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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-Components
#1: Protein | Mass: 35989.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ocimum basilicum (sweet basil) / Gene: EGS1 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15GI4 #2: Chemical | #3: 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: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M sodium succinate, 21% PEG 3350, 0.3 M KCl, 2 mM dithiothreitol, 5 mM NADP+, pH 5.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 10, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→34.12 Å / Num. obs: 87251 / % possible obs: 81.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 4.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2QW8 Resolution: 1.5→33.08 Å / FOM work R set: 0.865 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 49.907 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.867 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→33.08 Å
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Refine LS restraints |
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Xplor file |
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