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- PDB-8qxq: PsiM in complex with SAH and psilocybin -

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Basic information

Entry
Database: PDB / ID: 8qxq
TitlePsiM in complex with SAH and psilocybin
ComponentsPsilocybin synthase
KeywordsTRANSFERASE / 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
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 / FOURIER SYNTHESIS / Resolution: 0.94 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
DepositionOct 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6295
Polymers35,8901
Non-polymers7404
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-19 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.342, 78.521, 83.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Psilocybin synthase / Psilocybin biosynthesis methyltransferase


Mass: 35889.578 Da / Num. of mol.: 1
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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-X8Q / [3-[2-(dimethylamino)ethyl]-1~{H}-indol-4-yl] dihydrogen phosphate


Mass: 284.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N2O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris/HCl pH 8.5, 20% PEG 8000, 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jun 29, 2023 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 0.94→15.44 Å / Num. obs: 211345 / % possible obs: 99.81 % / Redundancy: 26.8 % / Biso Wilson estimate: 11.17 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1082 / Rpim(I) all: 0.0212 / Rrim(I) all: 0.1103 / Net I/σ(I): 13.36
Reflection shellResolution: 0.94→0.9736 Å / Redundancy: 26.9 % / Rmerge(I) obs: 4.584 / Mean I/σ(I) obs: 0.53 / Num. unique obs: 20765 / CC1/2: 0.383 / CC star: 0.745 / Rpim(I) all: 0.8985 / Rrim(I) all: 4.673 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia23.12.0data reduction
xia23.12.0data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.94→15.44 Å / SU ML: 0.1239 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.1338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1494 3178 1.51 %
Rwork0.1365 207882 -
obs0.1367 211060 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.66 Å2
Refinement stepCycle: LAST / Resolution: 0.94→15.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 47 451 2995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332902
X-RAY DIFFRACTIONf_angle_d1.32263995
X-RAY DIFFRACTIONf_chiral_restr0.1065436
X-RAY DIFFRACTIONf_plane_restr0.018537
X-RAY DIFFRACTIONf_dihedral_angle_d13.28691141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.94-0.950.37741360.37278776X-RAY DIFFRACTION97.57
0.95-0.970.3591370.34698947X-RAY DIFFRACTION99.68
0.97-0.980.30791520.3158969X-RAY DIFFRACTION99.97
0.98-10.26061280.28158953X-RAY DIFFRACTION100
1-1.020.27121480.25158962X-RAY DIFFRACTION100
1.02-1.040.28061120.23038981X-RAY DIFFRACTION99.97
1.04-1.060.21511470.19868999X-RAY DIFFRACTION99.92
1.06-1.080.18981460.17838971X-RAY DIFFRACTION99.99
1.08-1.110.20171370.16538989X-RAY DIFFRACTION99.95
1.11-1.140.1711220.15859040X-RAY DIFFRACTION99.98
1.14-1.170.16421520.13688982X-RAY DIFFRACTION99.93
1.17-1.20.13541350.12879022X-RAY DIFFRACTION99.9
1.2-1.240.1561240.12568993X-RAY DIFFRACTION99.92
1.24-1.280.13981490.12149024X-RAY DIFFRACTION99.98
1.28-1.340.12491430.11779051X-RAY DIFFRACTION99.98
1.34-1.40.1411330.11558996X-RAY DIFFRACTION99.87
1.4-1.470.13651350.10649088X-RAY DIFFRACTION99.87
1.47-1.560.10071450.09719068X-RAY DIFFRACTION100
1.56-1.680.13331340.1019108X-RAY DIFFRACTION99.97
1.68-1.850.12151430.10959113X-RAY DIFFRACTION100
1.85-2.120.12161380.11859171X-RAY DIFFRACTION99.99
2.12-2.670.1411400.13389208X-RAY DIFFRACTION99.91
2.67-15.440.15511420.14249471X-RAY DIFFRACTION99.14

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