+Open data
-Basic information
Entry | Database: PDB / ID: 2qx7 | ||||||
---|---|---|---|---|---|---|---|
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 / molecular replacement / Resolution: 1.75 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qx7.cif.gz | 147 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qx7.ent.gz | 115.2 KB | Display | PDB format |
PDBx/mmJSON format | 2qx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/2qx7 ftp://data.pdbj.org/pub/pdb/validation_reports/qx/2qx7 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2qw8C 2qysC 2qzzC 2r2gC 2r6jC 1qycS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | biological unit is a monomer (half of the asymmetric unit) |
-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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.11 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2005 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.75 Å / Num. obs: 68896 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.99 % / Biso Wilson estimate: 26.18 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.54 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.83 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3 / Num. measured obs: 55088 / Num. unique obs: 9455 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 0.568 / Cor.coef. Fo:Fc: 0.495
|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QYC Resolution: 1.75→42.05 Å / FOM work R set: 0.744 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 50.005 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.074 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→42.05 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|