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Yorodumi- PDB-3c1o: The multiple phenylpropene synthases in both Clarkia breweri and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c1o | ||||||
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Title | The multiple phenylpropene synthases in both Clarkia breweri and Petunia hybrida represent two distinct lineages | ||||||
Components | eugenol synthase | ||||||
Keywords | OXIDOREDUCTASE / eugenol / phenylpropene / PIP reductase / short-chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clarkia breweri (fairy fans) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 | 3c1o.cif.gz | 82 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c1o.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 3c1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c1o_validation.pdf.gz | 712.5 KB | Display | wwPDB validaton report |
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Full document | 3c1o_full_validation.pdf.gz | 717 KB | Display | |
Data in XML | 3c1o_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3c1o_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/3c1o ftp://data.pdbj.org/pub/pdb/validation_reports/c1/3c1o | HTTPS FTP |
-Related 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 36341.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clarkia breweri (fairy fans) / Gene: EGS1 / Plasmid: pHIS8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0VWT0*PLUS |
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#2: Chemical | ChemComp-NAP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1 M sodium citrate, 20% (w/v) PEG 4000, 20% (v/v) isopropanol, 2 mM dithiothreitol, 5 mM NADP+, pH 5.4, 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: Nov 2, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.434→50.572 Å / Num. obs: 26859 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.482 / Cor.coef. Fo:Fc: 0.412
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.9 Å / FOM work R set: 0.879 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 45.886 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.385 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→33.9 Å
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Refine LS restraints |
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Xplor file |
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