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Yorodumi- PDB-8xdr: O-methyltransferase from Lycoris aurea complexed with Mg, SAH, an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xdr | |||||||||
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Title | O-methyltransferase from Lycoris aurea complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde | |||||||||
Components | O-methyltransferase family protein | |||||||||
Keywords | TRANSFERASE / O-methyltransferase family protein / LaOMT | |||||||||
Function / homology | Protocatechuic aldehyde / S-ADENOSYL-L-HOMOCYSTEINE Function and homology information | |||||||||
Biological species | Lycoris aurea (golden hurricane-lily) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 | 8xdr.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xdr.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 8xdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xdr_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8xdr_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8xdr_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 8xdr_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/8xdr ftp://data.pdbj.org/pub/pdb/validation_reports/xd/8xdr | HTTPS FTP |
-Related structure data
Related structure data | 8xdoC 8xdpC 8xdqC 8xdsC 8xdtC 8xduC 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27423.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lycoris aurea (golden hurricane-lily) / Production host: Escherichia coli M15 (bacteria) |
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-Non-polymers , 6 types, 387 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-H6N / | #7: 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: 2.13 Å3/Da / Density % sol: 42.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 15% (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 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: 1.83→47.38 Å / Num. obs: 78525 / % possible obs: 98.6 % / Redundancy: 8.3 % / Biso Wilson estimate: 23.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.83→1.87 Å / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2469 / CC1/2: 0.735 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→47.38 Å / SU ML: 0.2111 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 21.0378 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: 28.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→47.38 Å
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Refine LS restraints |
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LS refinement shell |
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