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- PDB-8pb4: PsiM in complex with SAH and norbaeocystin, orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 8pb4
TitlePsiM in complex with SAH and norbaeocystin, orthorhombic crystal form
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
S-ADENOSYL-L-HOMOCYSTEINE / : / Psilocybin synthase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 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)36,6015
Polymers35,8901
Non-polymers7124
Water7,981443
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 area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.234, 78.266, 83.766
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / 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.: 443 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
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: 0.91→15.39 Å / Num. obs: 230836 / % possible obs: 99.06 % / Redundancy: 13.4 % / Biso Wilson estimate: 11.02 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08633 / Rpim(I) all: 0.02445 / Rrim(I) all: 0.08979 / Net I/σ(I): 10.37
Reflection shellResolution: 0.91→0.9427 Å / Redundancy: 13.6 % / Rmerge(I) obs: 3.04 / Mean I/σ(I) obs: 0.31 / Num. unique obs: 20907 / CC1/2: 0.383 / CC star: 0.744 / Rpim(I) all: 0.857 / Rrim(I) all: 3.16 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia23.12.0data scaling
xia23.12.0data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.91→15.39 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1558 3439 1.5 %
Rwork0.1443 --
obs0.1444 228792 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.17 Å2
Refinement stepCycle: LAST / Resolution: 0.91→15.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 45 443 2985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112901
X-RAY DIFFRACTIONf_angle_d1.2683993
X-RAY DIFFRACTIONf_dihedral_angle_d14.0061117
X-RAY DIFFRACTIONf_chiral_restr0.099436
X-RAY DIFFRACTIONf_plane_restr0.019530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.91-0.920.44271220.4197397X-RAY DIFFRACTION83
0.92-0.940.41911240.40438668X-RAY DIFFRACTION96
0.94-0.950.38321310.3869039X-RAY DIFFRACTION100
0.95-0.960.35261330.36819048X-RAY DIFFRACTION100
0.96-0.980.36261410.34048955X-RAY DIFFRACTION100
0.98-10.34341430.30728990X-RAY DIFFRACTION100
1-1.020.27261470.26949069X-RAY DIFFRACTION100
1.02-1.030.26361240.23989028X-RAY DIFFRACTION100
1.03-1.060.22711470.20059023X-RAY DIFFRACTION100
1.06-1.080.20191270.18939015X-RAY DIFFRACTION100
1.08-1.10.18861480.17419083X-RAY DIFFRACTION100
1.1-1.130.18011420.17299013X-RAY DIFFRACTION100
1.13-1.160.16681380.15019045X-RAY DIFFRACTION100
1.16-1.20.17261270.13849105X-RAY DIFFRACTION100
1.2-1.240.16161480.1469016X-RAY DIFFRACTION100
1.24-1.280.17051340.13619065X-RAY DIFFRACTION100
1.28-1.330.1631440.1419115X-RAY DIFFRACTION100
1.33-1.390.14691340.1319076X-RAY DIFFRACTION100
1.39-1.460.15681400.11929124X-RAY DIFFRACTION100
1.46-1.560.13411370.10699113X-RAY DIFFRACTION100
1.56-1.680.11631420.10289176X-RAY DIFFRACTION100
1.68-1.840.16461400.11179158X-RAY DIFFRACTION100
1.84-2.110.13111370.12229216X-RAY DIFFRACTION100
2.11-2.660.13461460.13369288X-RAY DIFFRACTION100
2.66-15.390.13441430.14119528X-RAY DIFFRACTION99

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