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Yorodumi- PDB-3c3x: The multiple phenylpropene synthases in both Clarkia breweri and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c3x | ||||||
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Title | The multiple phenylpropene synthases in both Clarkia breweri and Petunia hybrida represent two distinct lineages | ||||||
Components | Eugenol synthase 1 | ||||||
Keywords | OXIDOREDUCTASE / eugenol / phenylpropene / PIP reductase / short-chain dehydrogenase/reductase / NADP / Phenylpropanoid metabolism | ||||||
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 / Resolution: 2.15 Å | ||||||
Authors | Louie, G.V. / Noel, J.P. / Bowman, M.E. | ||||||
Citation | Journal: Plant J. / Year: 2008 Title: The multiple phenylpropene synthases in both Clarkia breweri and Petunia hybrida represent two distinct protein lineages. Authors: Koeduka, T. / Louie, G.V. / Orlova, I. / Kish, C.M. / Ibdah, M. / Wilkerson, C.G. / Bowman, M.E. / Baiga, T.J. / Noel, J.P. / Dudareva, N. / Pichersky, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c3x.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c3x.ent.gz | 108.4 KB | Display | PDB format |
PDBx/mmJSON format | 3c3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/3c3x ftp://data.pdbj.org/pub/pdb/validation_reports/c3/3c3x | HTTPS FTP |
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-Related structure data
Related structure data | 3c1oC 2qx7S 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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1 |
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2 |
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Unit cell |
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Details | Biological unit is a monomer (half of the asymmetric unit) |
-Components
#1: Protein | Mass: 35991.438 Da / Num. of mol.: 2 / Mutation: F85V, I88Y 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, Oxidoreductases #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: 2.32 Å3/Da / Density % sol: 46.91 % |
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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: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.518→57.947 Å / Num. obs: 45628 / % possible obs: 85.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Rsym value: 0.18 / Net I/σ(I): 3.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.015
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-Processing
Software |
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Refinement | Starting model: PDB entry 2QX7 Resolution: 2.15→57.9 Å / FOM work R set: 0.7 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 48.716 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.841 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→57.9 Å
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Refine LS restraints |
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Xplor file |
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