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- PDB-8pb7: PsiM in complex with sinefungin and baeocystin -

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Basic information

Entry
Database: PDB / ID: 8pb7
TitlePsiM in complex with sinefungin and baeocystin
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
SINEFUNGIN / : / Psilocybin synthase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.92 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

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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)36,6125
Polymers35,8901
Non-polymers7234
Water7,891438
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 area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.371, 78.244, 83.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XPN / Baeocystin / [3-[2-(methylamino)ethyl]-1~{H}-indol-4-yl] dihydrogen phosphate


Mass: 270.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O4P / 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.: 438 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
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: 0.6888 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 4, 2023 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 0.92→15.41 Å / Num. obs: 224244 / % possible obs: 99.53 % / Redundancy: 13.5 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08247 / Rpim(I) all: 0.02327 / Rrim(I) all: 0.08574 / Net I/σ(I): 10.88
Reflection shellResolution: 0.92→0.953 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.596 / Mean I/σ(I) obs: 0.33 / Num. unique obs: 21394 / CC1/2: 0.441 / CC star: 0.782 / Rpim(I) all: 0.7213 / Rrim(I) all: 2.696 / % possible all: 96.22

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia23.12.0data scaling
xia23.12.0data reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 0.92→15.41 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1612 3343 1.5 %
Rwork0.1462 --
obs0.1464 223269 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.37 Å2
Refinement stepCycle: LAST / Resolution: 0.92→15.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 47 438 2982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092914
X-RAY DIFFRACTIONf_angle_d1.1054012
X-RAY DIFFRACTIONf_dihedral_angle_d13.4231094
X-RAY DIFFRACTIONf_chiral_restr0.086443
X-RAY DIFFRACTIONf_plane_restr0.013526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.930.40251410.41698336X-RAY DIFFRACTION92
0.93-0.950.43151170.40469071X-RAY DIFFRACTION99
0.95-0.960.40971270.38629134X-RAY DIFFRACTION100
0.96-0.980.36371470.35949081X-RAY DIFFRACTION100
0.98-0.990.33091490.33689119X-RAY DIFFRACTION100
0.99-1.010.30851310.29089167X-RAY DIFFRACTION100
1.01-1.030.32541370.26079126X-RAY DIFFRACTION100
1.03-1.050.27081530.22029114X-RAY DIFFRACTION100
1.05-1.080.21591270.20049169X-RAY DIFFRACTION100
1.08-1.10.1951470.18179118X-RAY DIFFRACTION100
1.1-1.130.20821420.18219134X-RAY DIFFRACTION100
1.13-1.160.18411360.15629154X-RAY DIFFRACTION100
1.16-1.190.16681290.14359138X-RAY DIFFRACTION100
1.19-1.230.14421380.13649222X-RAY DIFFRACTION100
1.23-1.280.14531530.1299140X-RAY DIFFRACTION100
1.28-1.330.16051270.12699220X-RAY DIFFRACTION100
1.33-1.390.16041470.12279176X-RAY DIFFRACTION100
1.39-1.460.12921440.11719193X-RAY DIFFRACTION100
1.46-1.550.13011410.10399235X-RAY DIFFRACTION100
1.55-1.670.1291400.10389246X-RAY DIFFRACTION100
1.67-1.840.12271430.11169280X-RAY DIFFRACTION100
1.84-2.10.1551400.12059329X-RAY DIFFRACTION100
2.1-2.650.14891390.14029394X-RAY DIFFRACTION100
2.65-15.410.15161480.14999630X-RAY DIFFRACTION99

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