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- PDB-8zim: Crystal structure of the methyltransferase PsiM in complex with S... -

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Basic information

Entry
Database: PDB / ID: 8zim
TitleCrystal structure of the methyltransferase PsiM in complex with SAH and Baeocystin
ComponentsPsilocybin synthase
KeywordsTRANSFERASE / norbaeocystin / baeocystin / psilocybin / methyltransferase / SAM / SAH
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: 1.4 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 14, 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

Downloads & links

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Assembly

Deposited unit
A: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5385
Polymers34,5531
Non-polymers9854
Water8,215456
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint4 kcal/mol
Surface area13450 Å2
Unit cell
Length a, b, c (Å)39.399, 58.327, 130.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-931-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Psilocybin synthase / Psilocybin biosynthesis methyltransferase


Mass: 34553.129 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

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Non-polymers , 5 types, 460 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 20% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 60183 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 11.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.014 / Rrim(I) all: 0.05 / Net I/σ(I): 30.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 9.2 / Num. unique obs: 8615 / CC1/2: 0.986 / Rpim(I) all: 0.07 / Rrim(I) all: 0.256 / % 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: 8ZIE

8zie


Resolution: 1.4→33.72 Å / SU ML: 0.1327 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1726 3047 5.07 %
Rwork0.1457 57045 -
obs0.147 60092 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.94 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 65 456 2949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612617
X-RAY DIFFRACTIONf_angle_d0.93013572
X-RAY DIFFRACTIONf_chiral_restr0.0789396
X-RAY DIFFRACTIONf_plane_restr0.0129462
X-RAY DIFFRACTIONf_dihedral_angle_d9.6087395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.24521410.15992521X-RAY DIFFRACTION99.96
1.42-1.450.19761200.15322570X-RAY DIFFRACTION99.85
1.45-1.470.20641440.14522567X-RAY DIFFRACTION99.85
1.47-1.50.21681390.13282566X-RAY DIFFRACTION99.96
1.5-1.530.18191360.13422516X-RAY DIFFRACTION99.85
1.53-1.560.17661460.13872557X-RAY DIFFRACTION99.96
1.56-1.590.19871250.13652572X-RAY DIFFRACTION99.93
1.59-1.630.20021290.14092580X-RAY DIFFRACTION99.96
1.63-1.670.19461340.14652585X-RAY DIFFRACTION99.96
1.67-1.710.19461390.14622584X-RAY DIFFRACTION99.96
1.71-1.760.20391410.15052539X-RAY DIFFRACTION99.96
1.76-1.820.18451280.15282576X-RAY DIFFRACTION99.93
1.82-1.890.2041220.15412619X-RAY DIFFRACTION99.85
1.89-1.960.18671390.15142570X-RAY DIFFRACTION99.96
1.96-2.050.19521600.14432551X-RAY DIFFRACTION99.93
2.05-2.160.1721440.14292616X-RAY DIFFRACTION99.96
2.16-2.290.1491270.13912590X-RAY DIFFRACTION99.96
2.29-2.470.15741550.14342614X-RAY DIFFRACTION99.89
2.47-2.720.18461410.15292618X-RAY DIFFRACTION100
2.72-3.110.17291530.15522622X-RAY DIFFRACTION100
3.11-3.920.14731370.13832702X-RAY DIFFRACTION100
3.92-33.720.13591470.14562810X-RAY DIFFRACTION99.73

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