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Open data
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Basic information
Entry | Database: PDB / ID: 8pb5 | ||||||
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Title | PsiM in complex with sinefungin and norbaeocystin | ||||||
![]() | Psilocybin synthase | ||||||
![]() | TRANSFERASE / Methyltransferase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Werten, S. / Hudspeth, J. / Rupp, B. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.7 KB | Display | ![]() |
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PDB format | ![]() | 186.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pb3C ![]() 8pb4C ![]() 8pb6C ![]() 8pb7C ![]() 8pb8C ![]() 8qxqC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 35889.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P0DPA9, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | ChemComp-SFG / | ||||
#3: Chemical | ChemComp-XP6 / Mass: 256.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N2O4P / Feature type: SUBJECT OF INVESTIGATION | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris/HCl pH 8.5, 20% PEG 8000, 200 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 4, 2023 / Details: Toroidal mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6888 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→12.92 Å / Num. obs: 247003 / % possible obs: 99.42 % / Redundancy: 26.9 % / Biso Wilson estimate: 11.33 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09517 / Rpim(I) all: 0.01863 / Rrim(I) all: 0.097 / Net I/σ(I): 13.39 |
Reflection shell | Resolution: 0.89→0.9218 Å / Redundancy: 27.1 % / Rmerge(I) obs: 4.42 / Mean I/σ(I) obs: 0.39 / Num. unique obs: 23421 / CC1/2: 0.431 / CC star: 0.776 / Rpim(I) all: 0.8593 / Rrim(I) all: 4.504 / % possible all: 95.79 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 17.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→12.92 Å
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Refine LS restraints |
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LS refinement shell |
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