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- PDB-9fmh: PsiM N247M in complex with SAH and norbaeocystin -

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Basic information

Entry
Database: PDB / ID: 9fmh
TitlePsiM N247M in complex with SAH and norbaeocystin
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
S-ADENOSYL-L-HOMOCYSTEINE / : / Psilocybin synthase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 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

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Assembly

Deposited unit
A: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6185
Polymers35,9071
Non-polymers7124
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-19 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.372, 78.543, 83.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 35906.672 Da / Num. of mol.: 1 / Mutation: N247M
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XP6 / Norbaeocystin / [3-(2-azanylethyl)-1~{H}-indol-4-yl] dihydrogen phosphate


Mass: 256.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N2O4P / 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.: 437 / 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: 2.26 Å3/Da / Density % sol: 45.62 % / 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: 0.9→18.49 Å / Num. obs: 238138 / % possible obs: 98.99 % / Redundancy: 13.5 % / Biso Wilson estimate: 9.63 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.31
Reflection shellResolution: 0.9→0.932 Å / Num. unique obs: 23091 / CC1/2: 0.4

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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: 0.9→18.49 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1481 1986 -
Rwork0.1378 --
obs0.1379 237900 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.9→18.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 45 437 2979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015
X-RAY DIFFRACTIONf_angle_d1.406
X-RAY DIFFRACTIONf_dihedral_angle_d7.643450
X-RAY DIFFRACTIONf_chiral_restr0.112439
X-RAY DIFFRACTIONf_plane_restr0.014533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.9213716277X-RAY DIFFRACTION97
0.92-0.950.29611400.29116558X-RAY DIFFRACTION98
0.95-0.980.29141360.264316582X-RAY DIFFRACTION98
0.98-1.010.23591470.209716622X-RAY DIFFRACTION98
1.01-1.0412716725X-RAY DIFFRACTION99
1.04-1.080.15611460.145116706X-RAY DIFFRACTION99
1.08-1.130.13671460.127116813X-RAY DIFFRACTION99
1.13-1.190.13491440.116616842X-RAY DIFFRACTION99
1.19-1.270.14181380.112516908X-RAY DIFFRACTION100
1.27-1.3715016970X-RAY DIFFRACTION100
1.37-1.50.13231360.108417035X-RAY DIFFRACTION100
1.5-1.720.12261490.109417079X-RAY DIFFRACTION100
1.72-2.170.14221420.130817236X-RAY DIFFRACTION100
2.17-18.490.14921480.143117561X-RAY DIFFRACTION99

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