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Yorodumi- PDB-3p9k: Crystal structure of perennial ryegrass LpOMT1 complexed with S-a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p9k | ||||||
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Title | Crystal structure of perennial ryegrass LpOMT1 complexed with S-adenosyl-L-homocysteine and coniferaldehyde | ||||||
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: 2.25 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 | 3p9k.cif.gz | 282.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p9k.ent.gz | 228.1 KB | Display | PDB format |
PDBx/mmJSON format | 3p9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/3p9k ftp://data.pdbj.org/pub/pdb/validation_reports/p9/3p9k | HTTPS FTP |
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-Related structure data
Related structure data | 3p9cC 3p9iSC 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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-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-CIY / ( #4: 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: 2.37 Å3/Da / Density % sol: 48.15 % |
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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 5000 monomethylether, 2 mM dithiothreitol, 2.5 mM S-adenosyl-L-homocysteine, 5 mM coniferaldehyde, 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: 2.25→48.693 Å / Num. obs: 78617 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rsym value: 0.118 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3P9I Resolution: 2.25→48.693 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7169 / 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: 30.688 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.12 Å2 / Biso mean: 34.915 Å2 / Biso min: 3.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→48.693 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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