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- PDB-9fmk: PsiM N247A in complex with sinefungin and baeocystin -

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Basic information

Entry
Database: PDB / ID: 9fmk
TitlePsiM N247A in complex with sinefungin and baeocystin
ComponentsPsilocybin synthase
KeywordsBIOSYNTHETIC PROTEIN / Methyltransferase / Rossmann fold / Complex
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 / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsHudspeth, J. / Rupp, B. / Werten, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI-5192 Austria
CitationJournal: Chembiochem / Year: 2024
Title: The Second Methylation in Psilocybin Biosynthesis Is Enabled by a Hydrogen Bonding Network Extending into the Secondary Sphere Surrounding the Methyltransferase Active Site.
Authors: Hudspeth, J. / Rogge, K. / Wagner, T. / Mull, M. / Hoffmeister, D. / Rupp, B. / Werten, S.
History
DepositionJun 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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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)36,5695
Polymers35,8471
Non-polymers7234
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-19 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.738, 78.406, 83.855
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: 35846.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Gene: psiM / Production host: Escherichia coli (E. coli)
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.: 533 / 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: 2.29 Å3/Da / Density % sol: 46.28 % / Description: orthorhombic
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 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 1.01→16.26 Å / Num. obs: 171703 / % possible obs: 99.85 % / Redundancy: 13.4 % / CC1/2: 0.997 / Net I/σ(I): 8.98
Reflection shellResolution: 1.01→1.05 Å / Num. unique obs: 16930 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→16.26 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1614 2000 1.17 %
Rwork0.1399 --
obs0.1401 171602 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.01→16.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 47 533 3074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.423
X-RAY DIFFRACTIONf_dihedral_angle_d9.253455
X-RAY DIFFRACTIONf_chiral_restr0.114457
X-RAY DIFFRACTIONf_plane_restr0.015549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.030.33761300.337511920X-RAY DIFFRACTION99
1.03-1.0614111972X-RAY DIFFRACTION100
1.06-1.090.30951450.255112004X-RAY DIFFRACTION100
1.09-1.130.22791400.218812013X-RAY DIFFRACTION100
1.13-1.170.2111490.18912048X-RAY DIFFRACTION100
1.17-1.220.19041450.174212059X-RAY DIFFRACTION100
1.22-1.270.16741390.160212069X-RAY DIFFRACTION100
1.27-1.340.17861470.146112040X-RAY DIFFRACTION100
1.34-1.420.15051350.136112149X-RAY DIFFRACTION100
1.42-1.530.14231450.11512100X-RAY DIFFRACTION100
1.53-1.690.1371480.106212157X-RAY DIFFRACTION100
1.69-1.930.13731390.111912198X-RAY DIFFRACTION100
1.93-2.430.14081480.120812299X-RAY DIFFRACTION100
2.43-16.260.1541490.133112574X-RAY DIFFRACTION99

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