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- PDB-8x4s: The L-tryptophan specific decarboxylase PsiD covalent bonding wit... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8x4s
TitleThe L-tryptophan specific decarboxylase PsiD covalent bonding 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
: / L-tryptophan decarboxylase
Similarity search - Component
Biological speciesPsilocybe cubensis (magic mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

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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
G: L-tryptophan decarboxylase
H: L-tryptophan decarboxylase
A: L-tryptophan decarboxylase
B: L-tryptophan decarboxylase
C: L-tryptophan decarboxylase
D: L-tryptophan decarboxylase
E: L-tryptophan decarboxylase
F: L-tryptophan decarboxylase
K: L-tryptophan decarboxylase
L: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,21018
Polymers297,81612
Non-polymers1,3946
Water8,413467
1
I: L-tryptophan decarboxylase
J: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8683
Polymers49,6362
Non-polymers2321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: L-tryptophan decarboxylase
H: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8683
Polymers49,6362
Non-polymers2321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: L-tryptophan decarboxylase
B: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8683
Polymers49,6362
Non-polymers2321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: L-tryptophan decarboxylase
D: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8683
Polymers49,6362
Non-polymers2321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: L-tryptophan decarboxylase
F: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8683
Polymers49,6362
Non-polymers2321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: L-tryptophan decarboxylase
L: L-tryptophan decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8683
Polymers49,6362
Non-polymers2321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.681, 122.502, 128.716
Angle α, β, γ (deg.)90.000, 99.770, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 57 through 61 or resid 63...
d_2ens_1(chain "C" and (resid 57 through 61 or resid 63...
d_3ens_1(chain "E" and (resid 57 through 61 or resid 63...
d_4ens_1(chain "G" and (resid 57 through 61 or resid 63...
d_5ens_1(chain "I" and (resid 57 through 61 or resid 63...
d_6ens_1(chain "K" and (resid 57 through 61 or resid 63...
d_1ens_2(chain "D" and (resid 404 through 415 or (resid 416...
d_2ens_2(chain "B" and resid 404 through 437)
d_3ens_2(chain "F" and (resid 404 through 418 or (resid 419...
d_4ens_2(chain "H" and (resid 404 through 410 or (resid 411...
d_5ens_2(chain "J" and resid 404 through 437)
d_6ens_2(chain "L" and (resid 404 through 418 or (resid 419...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LEULEUILEILEAE57 - 6157 - 61
d_12ens_1GLUGLUPHEPHEAE63 - 10363 - 103
d_13ens_1LYSLYSASPASPAE105 - 111105 - 111
d_14ens_1GLYGLYTHRTHRAE113 - 126113 - 126
d_15ens_1ALAALAGLNGLNAE128 - 136128 - 136
d_16ens_1LEULEULYSLYSAE138 - 143138 - 143
d_17ens_1LEULEUARGARGAE145 - 216145 - 216
d_18ens_1PHEPHEPHEPHEAE218 - 260218 - 260
d_19ens_1GLYGLYASNASNAE262 - 331262 - 331
d_110ens_1ASPASPGLYGLYAE334 - 402334 - 402
d_21ens_1LEULEUILEILECG57 - 6157 - 61
d_22ens_1GLUGLUPHEPHECG63 - 10363 - 103
d_23ens_1LYSLYSASPASPCG105 - 111105 - 111
d_24ens_1GLYGLYTHRTHRCG113 - 126113 - 126
d_25ens_1ALAALAGLNGLNCG128 - 136128 - 136
d_26ens_1LEULEULYSLYSCG138 - 143138 - 143
d_27ens_1LEULEUARGARGCG145 - 216145 - 216
d_28ens_1PHEPHEPHEPHECG218 - 260218 - 260
d_29ens_1GLYGLYASNASNCG262 - 331262 - 331
d_210ens_1ASPASPGLYGLYCG334 - 402334 - 402
d_31ens_1LEULEUILEILEEI57 - 6157 - 61
d_32ens_1GLUGLUPHEPHEEI63 - 10363 - 103
d_33ens_1LYSLYSASPASPEI105 - 111105 - 111
d_34ens_1GLYGLYTHRTHREI113 - 126113 - 126
d_35ens_1ALAALAGLNGLNEI128 - 136128 - 136
d_36ens_1LEULEULYSLYSEI138 - 143138 - 143
d_37ens_1LEULEUARGARGEI145 - 216145 - 216
d_38ens_1PHEPHEPHEPHEEI218 - 260218 - 260
d_39ens_1GLYGLYASNASNEI262 - 331262 - 331
d_310ens_1ASPASPGLYGLYEI334 - 402334 - 402
d_41ens_1LEULEUILEILEGC57 - 6157 - 61
d_42ens_1GLUGLUPHEPHEGC63 - 10363 - 103
d_43ens_1LYSLYSASPASPGC105 - 111105 - 111
d_44ens_1GLYGLYTHRTHRGC113 - 126113 - 126
d_45ens_1ALAALAGLNGLNGC128 - 136128 - 136
d_46ens_1LEULEULYSLYSGC138 - 143138 - 143
d_47ens_1LEULEUARGARGGC145 - 216145 - 216
d_48ens_1PHEPHEPHEPHEGC218 - 260218 - 260
d_49ens_1GLYGLYASNASNGC262 - 331262 - 331
d_410ens_1ASPASPGLYGLYGC334 - 402334 - 402
d_51ens_1LEULEUILEILEIA57 - 6157 - 61
d_52ens_1GLUGLUPHEPHEIA63 - 10363 - 103
d_53ens_1LYSLYSASPASPIA105 - 111105 - 111
d_54ens_1GLYGLYTHRTHRIA113 - 126113 - 126
d_55ens_1ALAALAGLNGLNIA128 - 136128 - 136
d_56ens_1LEULEULYSLYSIA138 - 143138 - 143
d_57ens_1LEULEUARGARGIA145 - 216145 - 216
d_58ens_1PHEPHEPHEPHEIA218 - 260218 - 260
d_59ens_1GLYGLYASNASNIA262 - 331262 - 331
d_510ens_1ASPASPGLYGLYIA334 - 402334 - 402
d_61ens_1LEULEUILEILEKK57 - 6157 - 61
d_62ens_1GLUGLUPHEPHEKK63 - 10363 - 103
d_63ens_1LYSLYSASPASPKK105 - 111105 - 111
d_64ens_1GLYGLYTHRTHRKK113 - 126113 - 126
d_65ens_1ALAALAGLNGLNKK128 - 136128 - 136
d_66ens_1LEULEULYSLYSKK138 - 143138 - 143
d_67ens_1LEULEUARGARGKK145 - 216145 - 216
d_68ens_1PHEPHEPHEPHEKK218 - 260218 - 260
d_69ens_1GLYGLYASNASNKK262 - 331262 - 331
d_610ens_1ASPASPGLYGLYKK334 - 402334 - 402
d_11ens_2SERSERLEULEUDH404 - 4371 - 34
d_21ens_2SERSERLEULEUBF404 - 4371 - 34
d_31ens_2SERSERLEULEUFJ404 - 4371 - 34
d_41ens_2SERSERLEULEUHD404 - 4371 - 34
d_51ens_2SERSERLEULEUJB404 - 4371 - 34
d_61ens_2SERSERLEULEULL404 - 4371 - 34

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999737753658, -0.0113765880908, -0.0198745353083), (-0.0166669462995, -0.956642826389, -0.290786374542), (-0.0157046748249, 0.291041364692, -0.95658156329)26.2735552958, 107.502098085, 15.513139422
2given(-0.855224213257, -0.153025447384, 0.495151247108), (0.261684430084, 0.697169703472, 0.667439632935), (-0.447339696552, 0.700383906878, -0.556192034171)11.026030627, -77.204928479, 42.4823727553
3given(-0.999918843828, 0.00202624137527, 0.0125777622448), (-0.00788395013846, 0.67710387609, -0.735845217634), (-0.0100074515942, -0.735884661703, -0.677032950145)30.8334792704, 11.6753274683, 75.3539116954
4given(0.999370628853, -0.0228793252579, -0.0271087192756), (-0.0040389869552, -0.832624431403, 0.55382329566), (-0.0352424852897, -0.553365243494, -0.832192810906)-4.11534937292, 44.5273277531, 33.3272149322
5given(0.874154203292, 0.427824889018, 0.229826659038), (-0.211702539196, -0.0902184899919, 0.97316116803), (0.437077182847, -0.899347812807, 0.0117067430952)-13.7948283487, -12.6918390033, 92.3996872194
6given(0.999511076251, -0.0254818322353, -0.0181186278974), (-0.0296661570142, -0.955915275636, -0.292140214509), (-0.00987560524535, 0.292534890281, -0.956203853992)27.1477283049, 107.700328556, 15.2422574889
7given(-0.862144929966, -0.150020217367, 0.483942201213), (0.261578532229, 0.686223393239, 0.678729788685), (-0.43391564988, 0.711752336809, -0.552381951041)11.3548724743, -76.6610766876, 41.3121985833
8given(-0.999867671065, 0.00946012140012, 0.0132342911598), (-0.0032853180644, 0.679340758058, -0.733815604308), (-0.0159325780909, -0.733761978127, -0.679219782111)30.3795170079, 11.3462065904, 75.3873132011
9given(0.999412732365, -0.0327891766795, -0.00995290306396), (-0.0218331145879, -0.833194421699, 0.55254897589), (-0.0264103293071, -0.552007178887, -0.833421003433)-4.01079939518, 44.941826644, 32.930440587
10given(0.865767609446, 0.431540474377, 0.253415203586), (-0.23505699196, -0.0963896142856, 0.967190391179), (0.44180839395, -0.896929128322, 0.0179855998805)-14.5953241639, -11.1900130997, 91.7748689122

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Components

#1: Protein
L-tryptophan decarboxylase / Psilocybin biosynthesis 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, L-tryptophan decarboxylase
#2: Protein/peptide
L-tryptophan decarboxylase / Psilocybin biosynthesis decarboxylase


Mass: 3951.634 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, L-tryptophan decarboxylase
#3: Chemical
ChemComp-A1LWG / (2~{R})-2-[2-(1~{H}-indol-3-yl)ethylamino]propanoic acid


Mass: 232.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 0.1 M Tris pH 8.5, 25% 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: 0.97853 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: 2.7→30 Å / Num. obs: 69245 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.079 / Rrim(I) all: 0.206 / Net I/σ(I): 7.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 10086 / CC1/2: 0.82 / Rpim(I) all: 0.308 / Rrim(I) all: 0.822 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
autoPROC1.20.1_4487data processing
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8X4Q

8x4q


Resolution: 2.7→29.77 Å / SU ML: 0.3361 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2329 3487 5.04 %
Rwork0.1984 65714 -
obs0.2001 69201 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.05 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18047 0 80 467 18594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009418608
X-RAY DIFFRACTIONf_angle_d1.073825273
X-RAY DIFFRACTIONf_chiral_restr0.0562721
X-RAY DIFFRACTIONf_plane_restr0.00973325
X-RAY DIFFRACTIONf_dihedral_angle_d16.00866608
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2EAX-RAY DIFFRACTIONNCS constraints0.0121255230445
ens_1d_3EAX-RAY DIFFRACTIONNCS constraints0.0041756256518
ens_1d_4EAX-RAY DIFFRACTIONNCS constraints0.0121255230445
ens_1d_5EAX-RAY DIFFRACTIONNCS constraints4.2111106205E-13
ens_1d_6EAX-RAY DIFFRACTIONNCS constraints0.0030204953913
ens_2d_2HDX-RAY DIFFRACTIONNCS constraints0.0087393732666
ens_2d_3HDX-RAY DIFFRACTIONNCS constraints5.15514611559E-11
ens_2d_4HDX-RAY DIFFRACTIONNCS constraints0
ens_2d_5HDX-RAY DIFFRACTIONNCS constraints6.90164152732E-12
ens_2d_6HDX-RAY DIFFRACTIONNCS constraints2.31698127489E-13
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3321390.28022654X-RAY DIFFRACTION99.64
2.74-2.780.35781530.28122569X-RAY DIFFRACTION99.82
2.78-2.820.34461140.27722634X-RAY DIFFRACTION99.67
2.82-2.860.36681340.2862621X-RAY DIFFRACTION99.57
2.86-2.910.35161540.2732584X-RAY DIFFRACTION99.78
2.91-2.960.27061230.26012673X-RAY DIFFRACTION99.68
2.96-3.010.32471430.25072593X-RAY DIFFRACTION99.78
3.01-3.070.29871290.23992680X-RAY DIFFRACTION99.79
3.07-3.130.28771370.23792563X-RAY DIFFRACTION99.78
3.13-3.20.25991360.24692642X-RAY DIFFRACTION99.78
3.2-3.270.27851310.24832631X-RAY DIFFRACTION99.82
3.28-3.360.28361500.22952614X-RAY DIFFRACTION99.78
3.36-3.450.28641460.22232618X-RAY DIFFRACTION99.75
3.45-3.550.2261310.21542633X-RAY DIFFRACTION99.78
3.55-3.660.24881560.20582599X-RAY DIFFRACTION99.89
3.66-3.790.22311420.20242654X-RAY DIFFRACTION99.79
3.79-3.950.22821490.19152610X-RAY DIFFRACTION99.71
3.95-4.120.20751410.18172623X-RAY DIFFRACTION99.82
4.12-4.340.19231250.15752657X-RAY DIFFRACTION99.82
4.34-4.610.16281270.15622640X-RAY DIFFRACTION99.82
4.61-4.970.18061460.14872618X-RAY DIFFRACTION99.89
4.97-5.460.19761470.15812656X-RAY DIFFRACTION99.64
5.46-6.250.18851380.17262634X-RAY DIFFRACTION99.6
6.25-7.850.18891620.16342645X-RAY DIFFRACTION99.65
7.85-29.770.1561340.14492669X-RAY DIFFRACTION98.14
Refinement TLS params.Method: refined / Origin x: 23.7140437583 Å / Origin y: 24.3759248216 Å / Origin z: 19.381366769 Å
111213212223313233
T0.232220725106 Å2-0.0144692934102 Å2-0.00391429638208 Å2-0.240280103686 Å20.0122000842131 Å2--0.232007511697 Å2
L0.0134845706741 °2-0.0113645953237 °2-0.00831635858761 °2-0.0128966598721 °20.0230226598027 °2---0.0474028397624 °2
S0.0135591257637 Å °0.00554917528998 Å °0.0176979204182 Å °0.0128198973227 Å °-0.0316089131456 Å °-0.0180080799139 Å °0.0264387952557 Å °0.00623527539133 Å °0.00288140723511 Å °
Refinement TLS groupSelection details: all

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