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- PDB-9gfs: PsiM in complex with SAH -

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Basic information

Entry
Database: PDB / ID: 9gfs
TitlePsiM in complex with SAH
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: 1.92 Å
AuthorsWerten, S. / Leitner, L. / Rupp, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundI-5192 Austria
CitationJournal: J.Appl.Crystallogr. / Year: 2025
Title: If you cannot see it, is it still there?
Authors: Leitner, L. / Hudspeth, J. / Werten, S. / Rupp, B.
History
DepositionAug 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 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
B: Psilocybin synthase
C: Psilocybin synthase
D: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,20211
Polymers143,5584
Non-polymers1,6447
Water7,044391
1
A: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2742
Polymers35,8901
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3093
Polymers35,8901
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3093
Polymers35,8901
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3093
Polymers35,8901
Non-polymers4202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.827, 139.317, 140.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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: 35889.578 Da / Num. of mol.: 4
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


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate / acetic acid pH 4.5, 40% ethylene glycol

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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: 1.92→44.36 Å / Num. obs: 130216 / % possible obs: 99.93 % / Redundancy: 27.2 % / Biso Wilson estimate: 39.08 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1587 / Rpim(I) all: 0.03082 / Rrim(I) all: 0.1617 / Net I/σ(I): 15.78
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 27.7 % / Rmerge(I) obs: 7.392 / Mean I/σ(I) obs: 0.59 / Num. unique obs: 12827 / CC1/2: 0.479 / CC star: 0.805 / Rpim(I) all: 1.421 / Rrim(I) all: 7.528 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASER2.8.3phasing
XDSJun 30, 2024data scaling
XDSJun 30, 2024data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→44.36 Å / SU ML: 0.2516 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.9091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2084 2609 2 %
Rwork0.1804 127539 -
obs0.1809 130148 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.98 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9026 0 107 391 9524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0179375
X-RAY DIFFRACTIONf_angle_d1.330912761
X-RAY DIFFRACTIONf_chiral_restr0.08091443
X-RAY DIFFRACTIONf_plane_restr0.01421654
X-RAY DIFFRACTIONf_dihedral_angle_d13.79953521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.32771330.32246602X-RAY DIFFRACTION99.9
1.95-1.990.35351400.31526621X-RAY DIFFRACTION99.9
1.99-2.030.32511390.29196650X-RAY DIFFRACTION99.96
2.03-2.080.31841310.27086665X-RAY DIFFRACTION99.99
2.08-2.130.30921340.25236665X-RAY DIFFRACTION99.94
2.13-2.180.26831350.23516643X-RAY DIFFRACTION99.97
2.18-2.240.28331340.22156661X-RAY DIFFRACTION99.96
2.24-2.30.25241380.21456653X-RAY DIFFRACTION100
2.3-2.380.2461370.20576682X-RAY DIFFRACTION99.99
2.38-2.460.20831380.18056684X-RAY DIFFRACTION100
2.46-2.560.20931380.17546701X-RAY DIFFRACTION100
2.56-2.680.24141400.17386671X-RAY DIFFRACTION99.99
2.68-2.820.18761320.17556710X-RAY DIFFRACTION99.99
2.82-30.2351400.18496750X-RAY DIFFRACTION99.99
3-3.230.21261400.18216720X-RAY DIFFRACTION100
3.23-3.550.22021360.18536746X-RAY DIFFRACTION99.99
3.55-4.070.17521400.1616787X-RAY DIFFRACTION100
4.07-5.120.15191410.13716867X-RAY DIFFRACTION100
5.12-44.360.18751430.16817061X-RAY DIFFRACTION99.46
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.60229527238-2.2561425196-1.907196886331.644585792021.699794326762.59819442443-0.0925090580705-0.265610328725-0.5440071840340.09086578529220.07739402766470.2142849794920.001652951304940.04155585786860.0438289034680.3763558345950.00675122913946-0.0518662855760.3369629662820.03194115932340.52788567034733.8513203787-30.3369413929-18.0401338464
21.70502477681-0.0429680542566-0.0193940279140.897594005293-0.04906682868691.351991243930.01075182850040.146011797449-0.112810740907-0.0264138330837-0.01013019929510.03329778573560.0252919053568-0.1192421631030.0004664114023420.3289136037580.0459676689647-0.06435837442070.35190856474-0.01138087080470.36338559986919.4733332851-14.3107856344-26.1281728108
33.831315985220.008659103047980.8100011810911.623694518541.456914423432.598480529060.158175277227-0.454714331367-0.1249134002030.182916784909-0.07388570316-0.01311149475670.0515178467621-0.114591765468-0.08894236095170.3393019659260.0422004244083-0.03338939264070.3330661222080.03478293727570.35225187048521.1221207063-10.5520982759-13.9336033796
44.92524942658-2.66146458066-0.03494644453932.09656762183-0.460329139411-0.0264550464528-0.0107069106102-0.3031768512150.3184240150960.01312297180490.00351783520786-0.186443641849-0.01880955488480.03426623646910.02373623865350.2917248455640.00768148156547-0.01563475882540.302552190213-0.0407359829630.36255080097256.5454896235-15.0278384548-18.1164071792
52.48676437919-0.1167155358390.5844866988512.771004760380.224223943521.744506220170.113809924609-0.0714725749449-0.0242100048508-0.0742162097233-0.179251918298-0.05803804233940.1775975338940.06086514696190.06460184797260.3266646173640.0456684570130.06236672744060.3179410100410.00753165910890.35590894542665.8183064804-30.5700562884-23.4976186747
60.976517881620.04121710142351.29602361255.17236482525-1.967851927174.604365482960.412317104258-1.38268757673-0.298555233731.26032042309-0.2983971312280.5872249079280.3564507447290.285142214149-0.07365274843790.770039281614-0.09786984406430.1359731268791.117083694290.1728748590170.57709955340258.8945853545-36.1801976144-11.3389861169
70.4658219845411.174534266840.4394977013663.820483195571.090107004480.3576816886010.0818752144727-0.290788007404-0.1632051148480.221560043678-0.000600105022606-0.2972834939770.07388608556160.113078438235-0.07955809885790.304887505306-0.047082565291-0.07291320816910.3897196591670.05127211963420.36511640029797.1749631175-28.7729845893-51.6591802643
82.74956514782.94395293115-0.5744524245224.65230249579-0.4126010534050.4232347615270.0766115421175-0.0418641100167-0.208538681294-0.0662392777242-0.0953651151089-0.342954468170.0754620073383-0.0190657922680.02503716566120.366870176167-0.0617501710083-0.05671653096440.2939808358770.01955083481320.32341973219486.8758108746-43.1133189714-55.4569034413
91.339651334130.4076256071040.01929381650572.349076777430.1316516144491.24820945691-0.06933964974460.144993638518-0.0104757674956-0.1302916420050.07712019822390.1158406226850.0557762715421-0.190293791541-0.008628847945680.3437697278-0.075279125091-0.05466679940790.3682490816250.006573642214870.31925132658974.1966116148-42.5105330761-58.6859733781
100.1070371892080.483144636698-0.2076510945972.5588384242-0.4182225906852.95397161659-0.0277982605747-0.04967052240180.1517681200210.1556214965830.1139558918350.2434979368060.0360860184534-0.0470945287605-0.09845683143460.288362084012-0.004267996268290.03498080733230.3120192205880.03561895295310.36737432390879.7873993037-10.8790463426-50.2420356805
111.29081440711-0.142854429919-0.302329738042.320098818940.1848467663581.01938336492-0.0377379732785-0.0310290044450.09453806352270.01502479207860.0906826630233-0.0549849402014-0.00792955798210.0769304800405-0.05150199803870.348232101351-0.0490262462609-0.0121081131040.3320128317130.03010949757180.32197905212496.12352844721.06664308304-61.5176409287
122.767166580332.28351531363-0.3960891906745.78855481008-1.837470160691.73137157430.260712627513-0.436483187341-0.03457011239030.853321487008-0.356623855765-0.278270955933-0.1649774015650.4088781067770.1082351193740.341083844859-0.0271454590054-0.05047744966780.338924365715-0.004999356411360.310963516804101.845731203-0.554124997771-49.422684825
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid -5:63)AA-5 - 631 - 69
22(chain A and resid 64:269)AA64 - 26970 - 258
33(chain A and resid 270:401)AA - B270 - 401259 - 1
44(chain B and resid 0:98)BC0 - 981 - 99
55(chain B and resid 99:299)BC99 - 299100 - 283
66(chain B and resid 300:401)BC - D300 - 401284 - 1
77(chain C and resid 0:44)CF0 - 441 - 45
88(chain C and resid 45:102)CF45 - 10246 - 103
99(chain C and resid 103:401)CF - G103 - 401104 - 1
1010(chain D and resid -7:58)DI-7 - 581 - 66
1111(chain D and resid 59:268)DI59 - 26867 - 257
1212(chain D and resid 269:401)DI - J269 - 401258 - 1

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