[English] 日本語
Yorodumi
- PDB-9gr7: PsiM in complex with sinefungin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gr7
TitlePsiM in complex with sinefungin
ComponentsPsilocybin synthase
KeywordsTRANSFERASE / psilocybin synthase / methyltransferase / sinefungin / Rossmann fold
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
SINEFUNGIN / Psilocybin synthase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsHudspeth, J. / Rupp, B. / Werten, S.
Funding support Austria, Germany, 2items
OrganizationGrant numberCountry
Austrian Science FundI 5192 Austria
German Research Foundation (DFG)456463463 Germany
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
DepositionSep 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 16, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Psilocybin synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3424
Polymers35,8901
Non-polymers4523
Water8,089449
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-21 kcal/mol
Surface area13850 Å2
Unit cell
Length a, b, c (Å)49.963, 78.370, 83.818
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

-
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 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DPA9, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 8000, 200 mM MgCl2, 2.1 mM psilocybin, 100 mM Tris pH 8.5

-
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: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.04→32.11 Å / Num. obs: 305456 / % possible obs: 99.98 % / Redundancy: 13.1 % / Biso Wilson estimate: 12.57 Å2 / CC1/2: 0.999 / CC star: 0.999 / Rmerge(I) obs: 0.05481 / Rpim(I) all: 0.01592 / Rrim(I) all: 0.05712 / Net I/σ(I): 18.22
Reflection shellResolution: 1.04→1.077 Å / Rmerge(I) obs: 1.249 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 15631 / CC1/2: 0.78 / CC star: 0.936 / Rpim(I) all: 0.3627

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.04→32.11 Å / SU ML: 0.0852 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 15.2717
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1641 15565 5.1 %
Rwork0.1455 289891 -
obs0.1464 305456 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.04→32.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 29 449 2972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082854
X-RAY DIFFRACTIONf_angle_d1.20453926
X-RAY DIFFRACTIONf_chiral_restr0.0968429
X-RAY DIFFRACTIONf_plane_restr0.0136531
X-RAY DIFFRACTIONf_dihedral_angle_d7.1811438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.04-1.050.28594660.29269689X-RAY DIFFRACTION99.85
1.05-1.060.30015280.2659658X-RAY DIFFRACTION99.99
1.06-1.080.24655170.25039673X-RAY DIFFRACTION99.99
1.08-1.090.21875350.22589644X-RAY DIFFRACTION100
1.09-1.110.2175130.20969681X-RAY DIFFRACTION100
1.11-1.120.22865100.19769651X-RAY DIFFRACTION100
1.12-1.140.20324940.18389787X-RAY DIFFRACTION99.97
1.14-1.150.20284890.17189588X-RAY DIFFRACTION99.95
1.15-1.170.19765150.16579679X-RAY DIFFRACTION99.98
1.17-1.190.15385150.1599730X-RAY DIFFRACTION100
1.19-1.210.17166060.15079509X-RAY DIFFRACTION99.99
1.21-1.230.17435610.1469630X-RAY DIFFRACTION100
1.23-1.260.15454900.13669698X-RAY DIFFRACTION100
1.26-1.280.14335650.13329617X-RAY DIFFRACTION99.97
1.28-1.310.15255240.12969657X-RAY DIFFRACTION99.99
1.31-1.340.15095670.1249581X-RAY DIFFRACTION100
1.34-1.370.14475430.12229676X-RAY DIFFRACTION99.98
1.37-1.410.14574870.11739678X-RAY DIFFRACTION99.99
1.41-1.450.13424640.11159771X-RAY DIFFRACTION100
1.45-1.50.13935430.10849604X-RAY DIFFRACTION100
1.5-1.550.13125340.10519663X-RAY DIFFRACTION99.97
1.55-1.620.13315410.10679615X-RAY DIFFRACTION99.98
1.62-1.690.14045520.11329637X-RAY DIFFRACTION99.97
1.69-1.780.14585060.12569689X-RAY DIFFRACTION99.98
1.78-1.890.14775210.13419656X-RAY DIFFRACTION99.99
1.89-2.040.1445410.13049638X-RAY DIFFRACTION100
2.04-2.240.164710.13949703X-RAY DIFFRACTION100
2.24-2.560.18234940.15099701X-RAY DIFFRACTION100
2.56-3.230.18734570.16299734X-RAY DIFFRACTION100
3.23-32.110.16255160.15339654X-RAY DIFFRACTION99.84

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more