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Yorodumi- PDB-8xdu: O-methyltransferase from Lycoris longituba M52S variant complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xdu | |||||||||
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Title | O-methyltransferase from Lycoris longituba M52S variant complexed with Mg and SAH | |||||||||
Components | norbelladine O-methyltransferase | |||||||||
Keywords | TRANSFERASE / O-methyltransferase family protein / LlOMT | |||||||||
Function / homology | Function and homology information norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation Similarity search - Function | |||||||||
Biological species | Lycoris longituba (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | |||||||||
Authors | Saw, Y.Y.H. / Nakashima, Y. / Morita, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Acs Catalysis / Year: 2024 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xdu.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xdu.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 8xdu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xdu_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 8xdu_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 8xdu_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 8xdu_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/8xdu ftp://data.pdbj.org/pub/pdb/validation_reports/xd/8xdu | HTTPS FTP |
-Related structure data
Related structure data | 8xdoC 8xdpC 8xdqC 8xdrC 8xdsC 8xdtC 8xdvC 8xdyC 8xe0C 8xe2C 8xe3C 8xe4C 8xe5C 8z8oC 8z8pC 8z8rC 8z8sC 8zfwC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27399.229 Da / Num. of mol.: 2 / Mutation: M52S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lycoris longituba (plant) / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A6B9TNK2 #2: Chemical | ChemComp-GOL / | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% (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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.052 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.052 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→48.54 Å / Num. obs: 72090 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 17.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2517 / CC1/2: 0.893 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→48.54 Å / SU ML: 0.179 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.1467 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: 19.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.92→48.54 Å
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Refine LS restraints |
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LS refinement shell |
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