[English] 日本語
Yorodumi
- PDB-8x4q: Apo structure of L-tryptophan specific decarboxylase PsiD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8x4q
TitleApo structure of L-tryptophan specific decarboxylase PsiD
Components(L-tryptophan decarboxylase) x 2
KeywordsOXIDOREDUCTASE / decarboxylase / psilocybin / L-tryptophan / psilocin / tryptamine
Function / homology
Function and homology information


L-tryptophan decarboxylase / L-tryptophan decarboxylase activity / psilocybin biosynthetic process / phosphatidylserine decarboxylase activity / phosphatidylethanolamine biosynthetic process / mitochondrion
Similarity search - Function
L-tryptophan decarboxylase PsiD-like / Phophatidylserine decarboxylase / Phosphatidylserine decarboxylase-related / Phosphatidylserine decarboxylase
Similarity search - Domain/homology
L-tryptophan decarboxylase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionNov 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-tryptophan decarboxylase
C: L-tryptophan decarboxylase
E: L-tryptophan decarboxylase
G: L-tryptophan decarboxylase
I: L-tryptophan decarboxylase
K: L-tryptophan decarboxylase
L: L-tryptophan decarboxylase
J: L-tryptophan decarboxylase
H: L-tryptophan decarboxylase
F: L-tryptophan decarboxylase
D: L-tryptophan decarboxylase
B: L-tryptophan decarboxylase


Theoretical massNumber of molelcules
Total (without water)298,23612
Polymers298,23612
Non-polymers00
Water15,637868
1
A: L-tryptophan decarboxylase
B: L-tryptophan decarboxylase


Theoretical massNumber of molelcules
Total (without water)49,7062
Polymers49,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-23 kcal/mol
Surface area16200 Å2
MethodPISA
2
C: L-tryptophan decarboxylase
D: L-tryptophan decarboxylase


Theoretical massNumber of molelcules
Total (without water)49,7062
Polymers49,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-23 kcal/mol
Surface area15810 Å2
MethodPISA
3
E: L-tryptophan decarboxylase
F: L-tryptophan decarboxylase


Theoretical massNumber of molelcules
Total (without water)49,7062
Polymers49,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-24 kcal/mol
Surface area15820 Å2
MethodPISA
4
G: L-tryptophan decarboxylase
H: L-tryptophan decarboxylase


Theoretical massNumber of molelcules
Total (without water)49,7062
Polymers49,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-19 kcal/mol
Surface area15750 Å2
MethodPISA
5
I: L-tryptophan decarboxylase
J: L-tryptophan decarboxylase


Theoretical massNumber of molelcules
Total (without water)49,7062
Polymers49,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-23 kcal/mol
Surface area16180 Å2
MethodPISA
6
K: L-tryptophan decarboxylase
L: L-tryptophan decarboxylase


Theoretical massNumber of molelcules
Total (without water)49,7062
Polymers49,7062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-23 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.285, 120.763, 128.456
Angle α, β, γ (deg.)90.000, 99.432, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
L-tryptophan decarboxylase


Mass: 45684.344 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Gene: psiD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DPA6
#2: Protein/peptide
L-tryptophan decarboxylase / Psilocybin biosynthesis decarboxylase


Mass: 4021.680 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The S403 was processed to a pyruvoyl group / Source: (gene. exp.) Psilocybe cubensis (magic mushroom) / Gene: psiD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DPA6, L-tryptophan decarboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium citrate pH 5.6, 30% w/v Polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / 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: 2.55→30 Å / Num. obs: 80722 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 37.49 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.07 / Rrim(I) all: 0.182 / Net I/σ(I): 9.1
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 11754 / CC1/2: 0.755 / Rpim(I) all: 0.34 / Rrim(I) all: 0.878 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
autoPROC1.20.1_4487data processing
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.55→29.37 Å / SU ML: 0.3198 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0393
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 4090 5.07 %
Rwork0.1722 76589 -
obs0.1747 80679 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.41 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18150 0 30 868 19048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007618656
X-RAY DIFFRACTIONf_angle_d0.893625311
X-RAY DIFFRACTIONf_chiral_restr0.05432715
X-RAY DIFFRACTIONf_plane_restr0.00893346
X-RAY DIFFRACTIONf_dihedral_angle_d6.62472483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.580.33091310.25882654X-RAY DIFFRACTION99.96
2.58-2.610.28331500.24392584X-RAY DIFFRACTION99.96
2.61-2.640.30531450.23752647X-RAY DIFFRACTION99.93
2.64-2.680.27731340.23742627X-RAY DIFFRACTION99.93
2.68-2.720.28431530.22812616X-RAY DIFFRACTION99.93
2.72-2.750.24741410.21842668X-RAY DIFFRACTION99.96
2.75-2.80.26381340.20632617X-RAY DIFFRACTION99.96
2.8-2.840.27061430.20382616X-RAY DIFFRACTION100
2.84-2.890.29861310.20972632X-RAY DIFFRACTION99.96
2.89-2.940.28171390.2112676X-RAY DIFFRACTION99.96
2.94-2.990.28471270.21842622X-RAY DIFFRACTION99.96
2.99-3.050.2771400.21282663X-RAY DIFFRACTION99.96
3.05-3.110.27021220.20712618X-RAY DIFFRACTION100
3.11-3.180.27411560.21082642X-RAY DIFFRACTION100
3.18-3.250.271410.20012594X-RAY DIFFRACTION100
3.25-3.330.27481390.19382666X-RAY DIFFRACTION100
3.33-3.420.2331560.19122596X-RAY DIFFRACTION100
3.42-3.520.22861330.18252654X-RAY DIFFRACTION99.86
3.52-3.630.23841220.1682661X-RAY DIFFRACTION99.96
3.64-3.760.21631400.16232655X-RAY DIFFRACTION100
3.76-3.910.19281520.15542634X-RAY DIFFRACTION99.93
3.91-4.090.1861460.14742626X-RAY DIFFRACTION100
4.09-4.310.1721420.13532657X-RAY DIFFRACTION99.96
4.31-4.580.20341350.13352656X-RAY DIFFRACTION100
4.58-4.930.17181410.12932634X-RAY DIFFRACTION100
4.93-5.420.17821420.13892659X-RAY DIFFRACTION99.82
5.42-6.20.20211390.15272664X-RAY DIFFRACTION99.96
6.2-7.790.18551610.14972656X-RAY DIFFRACTION99.96
7.79-29.370.1651550.13522695X-RAY DIFFRACTION99.3
Refinement TLS params.Method: refined / Origin x: -22.7452443195 Å / Origin y: -3.02823465971 Å / Origin z: 32.9501162156 Å
111213212223313233
T0.215370723372 Å2-0.00578016033594 Å2-0.0146048716575 Å2-0.206523051865 Å20.0065700167341 Å2--0.220154456457 Å2
L0.129815089746 °20.00277737045156 °2-0.0864593679605 °2-0.0939426813878 °20.104630416692 °2--0.202456345045 °2
S0.00283665188483 Å °-0.0166999473194 Å °0.0126136714709 Å °0.0126198073539 Å °0.0187844440467 Å °-0.0267564125411 Å °-0.000260732794135 Å °0.0431847523588 Å °-0.0205112012782 Å °
Refinement TLS groupSelection details: all

+
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