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Yorodumi- PDB-3p9i: Crystal structure of perennial ryegrass LpOMT1 complexed with S-a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p9i | ||||||
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Title | Crystal structure of perennial ryegrass LpOMT1 complexed with S-adenosyl-L-homocysteine and sinapaldehyde | ||||||
Components | Caffeic acid O-methyltransferase | ||||||
Keywords | TRANSFERASE / S-adenosylmethionine dependent O-methyltransferase | ||||||
Function / homology | Function and homology information : / catechol O-methyltransferase activity / : / : / catechol O-methyltransferase / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | Lolium perenne (perennial ryegrass) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Louie, G.V. / Noel, J.P. / Bowman, M.E. | ||||||
Citation | Journal: Plant Cell / Year: 2010 Title: Structure-Function Analyses of a Caffeic Acid O-Methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference. Authors: Louie, G.V. / Bowman, M.E. / Tu, Y. / Mouradov, A. / Spangenberg, G. / 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 | 3p9i.cif.gz | 296.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p9i.ent.gz | 238.4 KB | Display | PDB format |
PDBx/mmJSON format | 3p9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p9i_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3p9i_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3p9i_validation.xml.gz | 60 KB | Display | |
Data in CIF | 3p9i_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p9i ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9i | HTTPS FTP |
-Related structure data
Related structure data | 3p9cSC 3p9kC 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: 39146.754 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lolium perenne (perennial ryegrass) / Gene: LpOMT1, OMT1 / Plasmid: pHIS8 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZTU2, catechol O-methyltransferase #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-SNY / ( #4: Chemical | ChemComp-BME / #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: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M sodium succinate, 28% (w/v) PEG monomethylether 5000, 2 mM dithiothreitol, 2.5 mM S-adenosyl-L-homocysteine, 5 mM sinapaldehyde, 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: Nov 8, 2008 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→47.071 Å / Num. obs: 139446 / % possible obs: 95.7 % / Redundancy: 3.1 % / Rsym value: 0.085 / Net I/σ(I): 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.554 / Cor.coef. Fo:Fc: 0.443
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3P9C Resolution: 1.85→47.07 Å / Occupancy max: 1 / Occupancy min: 0.33 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Maximum likelihood
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Solvent computation | Bsol: 44.2186 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.01 Å2 / Biso mean: 28.3449 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→47.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å
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Xplor file |
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