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- PDB-8zia: The L-tryptophan specific decarboxylase PsiD(50-439) in complex w... -

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Basic information

Entry
Database: PDB / ID: 8zia
TitleThe L-tryptophan specific decarboxylase PsiD(50-439) in complex with tryptamine
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
2-(1H-INDOL-3-YL)ETHANAMINE / L-tryptophan decarboxylase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 13, 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
I: L-tryptophan decarboxylase
J: L-tryptophan decarboxylase
A: L-tryptophan decarboxylase
B: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0646
Polymers88,7444
Non-polymers3202
Water16,628923
1
I: L-tryptophan decarboxylase
J: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5323
Polymers44,3722
Non-polymers1601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-25 kcal/mol
Surface area16070 Å2
MethodPISA
2
A: L-tryptophan decarboxylase
B: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5323
Polymers44,3722
Non-polymers1601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-25 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.277, 59.265, 104.138
Angle α, β, γ (deg.)90.000, 93.464, 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

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Components

#1: Protein L-tryptophan decarboxylase / Psilocybin biosynthesis decarboxylase


Mass: 40350.324 Da / Num. of mol.: 2
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, L-tryptophan decarboxylase
#2: Protein/peptide L-tryptophan decarboxylase / Psilocybin biosynthesis decarboxylase


Mass: 4021.680 Da / Num. of mol.: 2
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, L-tryptophan decarboxylase
#3: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE


Mass: 160.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 124004 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.05 / Net I/σ(I): 20.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 18007 / CC1/2: 0.93 / Rpim(I) all: 0.224 / Rrim(I) all: 0.587 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8X4Q

8x4q


Resolution: 1.6→35.51 Å / SU ML: 0.1774 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.6534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.181 6317 5.1 %
Rwork0.164 117630 -
obs0.1649 123947 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.37 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 34 923 7089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556335
X-RAY DIFFRACTIONf_angle_d0.80518584
X-RAY DIFFRACTIONf_chiral_restr0.0559907
X-RAY DIFFRACTIONf_plane_restr0.0081135
X-RAY DIFFRACTIONf_dihedral_angle_d15.92362312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.35641980.32413890X-RAY DIFFRACTION99.83
1.62-1.640.32632180.27923891X-RAY DIFFRACTION99.78
1.64-1.660.26821910.25783914X-RAY DIFFRACTION99.85
1.66-1.680.26892060.23063921X-RAY DIFFRACTION99.81
1.68-1.70.22652260.21963868X-RAY DIFFRACTION99.9
1.7-1.720.21642240.20343844X-RAY DIFFRACTION99.88
1.72-1.750.19022090.1913940X-RAY DIFFRACTION99.86
1.75-1.770.21172120.18813909X-RAY DIFFRACTION99.95
1.77-1.80.19952210.18043936X-RAY DIFFRACTION99.95
1.8-1.830.20512190.18273838X-RAY DIFFRACTION99.98
1.83-1.860.20752200.17613915X-RAY DIFFRACTION99.9
1.86-1.90.19772120.18373899X-RAY DIFFRACTION99.73
1.9-1.930.21932110.18733900X-RAY DIFFRACTION99.88
1.93-1.970.22542090.19273904X-RAY DIFFRACTION99.93
1.97-2.020.20271750.17723931X-RAY DIFFRACTION99.98
2.02-2.060.20051980.16883927X-RAY DIFFRACTION99.93
2.06-2.110.19592020.16613955X-RAY DIFFRACTION99.98
2.11-2.170.20382090.16583916X-RAY DIFFRACTION99.93
2.17-2.240.18652140.16773870X-RAY DIFFRACTION99.98
2.24-2.310.18752150.16293945X-RAY DIFFRACTION99.9
2.31-2.390.16452040.16943938X-RAY DIFFRACTION99.95
2.39-2.490.18382050.173946X-RAY DIFFRACTION99.9
2.49-2.60.20812120.1683890X-RAY DIFFRACTION99.9
2.6-2.740.1932200.16743944X-RAY DIFFRACTION99.95
2.74-2.910.16722360.16413912X-RAY DIFFRACTION99.88
2.91-3.130.17412100.16313949X-RAY DIFFRACTION99.71
3.13-3.450.17252210.15343920X-RAY DIFFRACTION99.76
3.45-3.940.14052000.14133980X-RAY DIFFRACTION99.45
3.94-4.970.14751940.13043996X-RAY DIFFRACTION99.69
4.97-35.510.15512260.14614042X-RAY DIFFRACTION99.16
Refinement TLS params.Method: refined / Origin x: -25.9346070549 Å / Origin y: 8.09174714363 Å / Origin z: -29.7639021722 Å
111213212223313233
T0.176655088156 Å20.000214669226742 Å2-0.0218122266848 Å2-0.142616652072 Å2-0.00748456352226 Å2--0.166243321591 Å2
L0.808644294096 °2-0.050737269209 °2-0.374713359288 °2-0.255659415125 °20.0510850423189 °2--0.595484765183 °2
S0.00322571626053 Å °-0.0966421955015 Å °0.0339224823235 Å °-0.00508499374821 Å °0.0198599588969 Å °-0.0174933069943 Å °0.0130195428212 Å °-0.015322443041 Å °-0.0186435906649 Å °
Refinement TLS groupSelection details: all

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