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Open data
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Basic information
Entry | Database: PDB / ID: 6i5q | ||||||
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Title | Papaver somniferum O-methyltransferase 1 | ||||||
![]() | O-methyltransferase 1 | ||||||
![]() | TRANSFERASE / SAM-dependent O-methyltransferase / Papaver somniferum / scoulerine / tetrahydrocolumbine / noscapine / benzylisoquinoline alkaloid | ||||||
Function / homology | ![]() tetrahydrocolumbamine 2-O-methyltransferase / benzyl isoquinoline alkaloid biosynthetic process / tetrahydrocolumbamine 2-O-methyltransferase activity / (S)-scoulerine 9-O-methyltransferase / (S)-scoulerine 9-O-methyltransferase activity / : / O-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cabry, M.P. / Offen, W.A. / Winzer, T. / Li, Y. / Graham, I.A. / Davies, G.J. / Saleh, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Papaver somniferum O-Methyltransferase 1 Reveals Initiation of Noscapine Biosynthesis with Implications for Plant Natural Product Methylation Authors: Cabry, M.P. / Offen, W.A. / Winzer, T.H. / Li, Y. / Graham, I.A. / Davies, G.J. / Saleh, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.5 KB | Display | ![]() |
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PDB format | ![]() | 210 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.7 KB | Display | ![]() |
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Full document | ![]() | 480.6 KB | Display | |
Data in XML | ![]() | 48.5 KB | Display | |
Data in CIF | ![]() | 66.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i5zC ![]() 6i6kC ![]() 6i6lC ![]() 6i6mC ![]() 6i6nC ![]() 1kyzS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 42888.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: O-methyltransferase sequence after cleavage with 3C-protease Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 3350, sodium citrate, bis-tris propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→97 Å / Num. obs: 43285 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.052 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.05→3.17 Å / Redundancy: 10 % / Rmerge(I) obs: 1.607 / Num. unique obs: 4464 / CC1/2: 0.592 / Rpim(I) all: 0.561 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KYZ Resolution: 3.05→97 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.882 / SU B: 16.598 / SU ML: 0.292 / Cross valid method: THROUGHOUT / ESU R: 2.204 / ESU R Free: 0.392 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THERE IS SOME UNMODELLED DENSITY BETWEEN THE SIDE CHAINS OF PHE156 AND HIS296 FOR EACH MOLECULE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.14 Å2
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Refinement step | Cycle: 1 / Resolution: 3.05→97 Å
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Refine LS restraints |
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