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- PDB-8zie: Crystal structure of the methyltransferase PsiM in its apo-form -

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Basic information

Entry
Database: PDB / ID: 8zie
TitleCrystal structure of the methyltransferase PsiM in its apo-form
ComponentsPsilocybin synthase
KeywordsTRANSFERASE / norbaeocystin / baeocystin / psilocybin / methyltransferase / SAM
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
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMeng, C.Y. / Wen, Y. / Guo, W.T. / Wu, B.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for psilocybin biosynthesis.
Authors: Meng, C. / Guo, W. / Xiao, C. / Wen, Y. / Zhu, X. / Zhang, Q. / Liang, Y. / Li, H. / Xu, S. / Qiu, Y. / Chen, H. / Lin, W.J. / Wu, B.
History
DepositionMay 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Psilocybin synthase


Theoretical massNumber of molelcules
Total (without water)34,4661
Polymers34,4661
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.627, 42.627, 260.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-429-

HOH

21A-613-

HOH

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Components

#1: Protein Psilocybin synthase / Psilocybin biosynthesis methyltransferase


Mass: 34466.051 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 BL21(DE3) (bacteria)
References: UniProt: P0DPA9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride, 0.1 M Tris pH 8.5, 30% w/v PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 38011 / % possible obs: 100 % / Redundancy: 18.5 % / Biso Wilson estimate: 24.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.021 / Rrim(I) all: 0.09 / Net I/σ(I): 18
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 19.2 % / Rmerge(I) obs: 1.089 / Mean I/σ(I) obs: 3 / Num. unique obs: 5426 / CC1/2: 0.926 / Rpim(I) all: 0.253 / Rrim(I) all: 1.118 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.6→36.92 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.9926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 1901 5.02 %
Rwork0.1989 35985 -
obs0.1998 37886 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 1.6→36.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 0 0 217 2323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742167
X-RAY DIFFRACTIONf_angle_d0.98492956
X-RAY DIFFRACTIONf_chiral_restr0.0573339
X-RAY DIFFRACTIONf_plane_restr0.0102382
X-RAY DIFFRACTIONf_dihedral_angle_d5.822297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.28881530.25772534X-RAY DIFFRACTION99.96
1.64-1.680.28611360.23992482X-RAY DIFFRACTION99.81
1.68-1.730.25511420.23992461X-RAY DIFFRACTION99.81
1.73-1.790.30261420.252538X-RAY DIFFRACTION99.89
1.79-1.850.26961080.26432583X-RAY DIFFRACTION99.96
1.85-1.930.2641190.22712503X-RAY DIFFRACTION99.96
1.93-2.020.28021260.21412557X-RAY DIFFRACTION99.96
2.02-2.120.18981430.20332530X-RAY DIFFRACTION99.93
2.12-2.260.2581400.21642560X-RAY DIFFRACTION99.93
2.26-2.430.21121460.2092523X-RAY DIFFRACTION100
2.43-2.670.23921180.21372631X-RAY DIFFRACTION100
2.67-3.060.22681380.20132610X-RAY DIFFRACTION99.96
3.06-3.850.20011230.17762655X-RAY DIFFRACTION100
3.86-36.920.17841670.17472818X-RAY DIFFRACTION99.97

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