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- PDB-8xdv: O-methyltransferase from Lycoris longituba M52S-F186Y variant com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xdv | |||||||||
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Title | O-methyltransferase from Lycoris longituba M52S-F186Y variant complexed with Mg and SAH | |||||||||
![]() | norbelladine O-methyltransferase | |||||||||
![]() | TRANSFERASE / O-methyltransferase family protein / LlOMT | |||||||||
Function / homology | ![]() norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Saw, Y.Y.H. / Nakashima, Y. / Morita, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases Authors: Hnin, S.Y.Y. / Nakashima, Y. / Kodama, T. / Morita, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.8 KB | Display | ![]() |
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PDB format | ![]() | 86 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8xdoC ![]() 8xdpC ![]() 8xdqC ![]() 8xdrC ![]() 8xdsC ![]() 8xdtC ![]() 8xduC ![]() 8xdyC ![]() 8xe0C ![]() 8xe2C ![]() 8xe3C ![]() 8xe4C ![]() 8xe5C ![]() 8z8oC ![]() 8z8pC ![]() 8z8rC ![]() 8z8sC ![]() 8zfwC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27415.229 Da / Num. of mol.: 2 / Mutation: M52S/F186Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 23% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 3, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.048 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→47.16 Å / Num. obs: 39195 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 41.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.038 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2027 / CC1/2: 0.891 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→47.16 Å
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Refine LS restraints |
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LS refinement shell |
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