+Open data
-Basic information
Entry | Database: PDB / ID: 6i5z | ||||||
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Title | Papaver somniferum O-methyltransferase | ||||||
Components | O-methyltransferase 1 | ||||||
Keywords | TRANSFERASE / SAM-dependent O-methyltransferase / Papaver somniferum / S-adenosyl methionine | ||||||
Function / homology | Function and homology information 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 | Papaver somniferum (opium poppy) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Davies, G.J. / Cabry, M.P. / Offen, W.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i5z.cif.gz | 269.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i5z.ent.gz | 212.1 KB | Display | PDB format |
PDBx/mmJSON format | 6i5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i5z_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6i5z_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6i5z_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 6i5z_validation.cif.gz | 67.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/6i5z ftp://data.pdbj.org/pub/pdb/validation_reports/i5/6i5z | HTTPS FTP |
-Related structure data
Related structure data | 6i5qSC 6i6kC 6i6lC 6i6mC 6i6nC 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: 42888.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Sequence after 3c-protease cleavage / Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: MT1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I3PLQ5, UniProt: I3V6A7*PLUS #2: Chemical | #3: Chemical | ChemComp-SAM / | |
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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: 3.16 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 2000, sodium succinate, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3→151.19 Å / Num. obs: 44411 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.034 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.873 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4590 / CC1/2: 0.53 / Rpim(I) all: 0.652 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I5Q Resolution: 3→101 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.896 / SU B: 20.581 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R: 1.638 / ESU R Free: 0.433 Details: THERE IS UNMODELLED DENSITY NEAR THE SIDE CHAIN OF ASP258 IN MOLECULE C
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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: 76.094 Å2
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Refinement step | Cycle: 1 / Resolution: 3→101 Å
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Refine LS restraints |
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