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Yorodumi- PDB-8xe5: norbelladine 4'-O-methyltransferase complexed with Mg, SAH, and 3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xe5 | |||||||||
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Title | norbelladine 4'-O-methyltransferase complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde | |||||||||
Components | Norbelladine 4'-O-methyltransferase | |||||||||
Keywords | TRANSFERASE / O-methyltransferase family protein / NpN4OMT | |||||||||
Function / homology | Function and homology information norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding Similarity search - Function | |||||||||
Biological species | Narcissus pseudonarcissus MK-2014 (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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 | 8xe5.cif.gz | 276.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xe5.ent.gz | 178 KB | Display | PDB format |
PDBx/mmJSON format | 8xe5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xe5_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 8xe5_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 8xe5_validation.xml.gz | 44.2 KB | Display | |
Data in CIF | 8xe5_validation.cif.gz | 62.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/8xe5 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/8xe5 | HTTPS FTP |
-Related structure data
Related structure data | 8xdoC 8xdpC 8xdqC 8xdrC 8xdsC 8xdtC 8xduC 8xdvC 8xdyC 8xe0C 8xe2C 8xe3C 8xe4C 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 27397.084 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Narcissus pseudonarcissus MK-2014 (plant) Gene: N4OMT / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A077EWA5 |
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-Non-polymers , 5 types, 764 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SAH / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.14 Å3/Da / Density % sol: 42.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 17% (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: 1.048 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 14, 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: 2.07→45.54 Å / Num. obs: 107759 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.07→2.13 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4364 / CC1/2: 0.687 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→45.54 Å / SU ML: 0.2408 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 22.2612 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: 22.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→45.54 Å
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Refine LS restraints |
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LS refinement shell |
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