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- PDB-8pb8: PsiM in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 8pb8
TitlePsiM in complex with SAH
ComponentsPsilocybin synthase
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


psilocybin synthase / 4-hydroxytryptamine 4-phosphate methyltransferase activity / psilocybin biosynthetic process / rRNA base methylation / Transferases; Transferring one-carbon groups; Methyltransferases / nucleus
Similarity search - Function
Methyltransferase METTL16/PsiM / RNA methyltransferase / METTL16/RlmF family / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Psilocybin synthase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.531 Å
AuthorsWerten, S. / Hudspeth, J. / Rupp, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI-5192 Austria
CitationJournal: 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
DepositionJun 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Dec 10, 2025Group: Atomic model / Data collection / Structure summary / Category: atom_site / chem_comp / pdbx_entry_details
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Psilocybin synthase
B: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1487
Polymers71,7792
Non-polymers1,3695
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Asymmetric unit contains 2 monomers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-8 kcal/mol
Surface area26850 Å2
Unit cell
Length a, b, c (Å)62.200, 62.200, 154.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Psilocybin synthase / Psilocybin biosynthesis methyltransferase


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 ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM bis-Tris propane pH 7.0, 30% PEG 300, 15% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 1, 2022 / Details: KB mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDS20220110data scaling
XDS20220110data reduction
PHASER2.8.2phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2518 1050 5.41 %
Rwork0.1977 --
obs0.2007 19403 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.7 Å2
Refinement stepCycle: LAST / Resolution: 2.531→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4892 0 85 21 4998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045087
X-RAY DIFFRACTIONf_angle_d0.6496907
X-RAY DIFFRACTIONf_dihedral_angle_d16.4361915
X-RAY DIFFRACTIONf_chiral_restr0.043773
X-RAY DIFFRACTIONf_plane_restr0.006898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.531-2.650.37231210.30292145X-RAY DIFFRACTION93
2.65-2.790.31321300.27752311X-RAY DIFFRACTION100
2.79-2.960.31821240.26722337X-RAY DIFFRACTION100
2.96-3.190.30211170.24182303X-RAY DIFFRACTION100
3.19-3.510.23811230.21042326X-RAY DIFFRACTION100
3.51-4.020.2411350.17032306X-RAY DIFFRACTION100
4.02-5.060.23641550.15582298X-RAY DIFFRACTION100
5.06-38.710.20741450.16942327X-RAY DIFFRACTION100

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