+Open data
-Basic information
Entry | Database: PDB / ID: 8pb8 | ||||||
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Title | PsiM in complex with SAH | ||||||
Components | Psilocybin synthase | ||||||
Keywords | TRANSFERASE / Methyltransferase | ||||||
Function / homology | Function and homology information psilocybin biosynthetic process / 4-hydroxytryptamine 4-phosphate methyltransferase activity / 23S rRNA (adenine(1618)-N(6))-methyltransferase activity / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / nucleus Similarity search - Function | ||||||
Biological species | Psilocybe cubensis (magic mushroom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.531 Å | ||||||
Authors | Werten, S. / Hudspeth, J. / Rupp, B. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Methyl transfer in psilocybin biosynthesis. Authors: Hudspeth, J. / Rogge, K. / Dorner, S. / Mull, M. / Hoffmeister, D. / Rupp, B. / Werten, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pb8.cif.gz | 239.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pb8.ent.gz | 193.2 KB | Display | PDB format |
PDBx/mmJSON format | 8pb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/8pb8 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pb8 | HTTPS FTP |
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-Related structure data
Related structure data | 8pb3C 8pb4C 8pb5C 8pb6C 8pb7C 8qxqC 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
#1: Protein | Mass: 35889.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Gene: psiM / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0DPA9, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #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: 2.09 Å3/Da / Density % sol: 41.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM bis-Tris propane pH 7.0, 30% PEG 300, 15% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 1, 2022 / Details: KB mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.531→38.71 Å / Num. obs: 19419 / % possible obs: 99.06 % / Redundancy: 6 % / Biso Wilson estimate: 45.23 Å2 / CC1/2: 0.977 / CC star: 0.994 / Rmerge(I) obs: 0.3496 / Rpim(I) all: 0.1543 / Rrim(I) all: 0.3828 / Net I/σ(I): 5.38 |
Reflection shell | Resolution: 2.531→2.622 Å / Redundancy: 6 % / Rmerge(I) obs: 2.197 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 1786 / CC1/2: 0.249 / CC star: 0.631 / Rpim(I) all: 0.9646 / Rrim(I) all: 2.402 / % possible all: 91.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.531→38.71 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.19 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.531→38.71 Å
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Refine LS restraints |
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LS refinement shell |
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