PDB-8pb3: PsiM in complex with SAH and norbaeocystin, monoclinic crystal form

ID or keywords:

Entry

Database: PDB / ID: 8pb3

Title

PsiM in complex with SAH and norbaeocystin, monoclinic crystal form

Components

Psilocybin synthase

Keywords

TRANSFERASE / 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

Biological species

Psilocybe cubensis (magic mushroom)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.18 Å

Authors

Werten, S. / Hudspeth, J. / Rupp, B.

Funding support

Austria, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Methyl transfer in psilocybin biosynthesis.
Authors: Hudspeth, J. / Rogge, K. / Dorner, S. / Mull, M. / Hoffmeister, D. / Rupp, B. / Werten, S.

History

Deposition	Jun 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2024	Group: Database references / Category: citation Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pb3.cif.gz	387.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8pb3.ent.gz	318.4 KB	Display	PDB format
PDBx/mmJSON format	8pb3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pb3_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8pb3_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8pb3_validation.xml.gz	31.5 KB	Display
Data in CIF	8pb3_validation.cif.gz	49 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pb/8pb3 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/8pb3	HTTPS FTP

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Related structure data

Related structure data	8pb4C 8pb5C 8pb6C 8pb7C 8pb8C 8qxqC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Psilocybin synthase

B: Psilocybin synthase

hetero molecules

73.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Asymmetric unit contains 2 monomers

Unit cell

Length a, b, c (Å)	166.040, 48.853, 115.452
Angle α, β, γ (deg.)	90.00, 131.40, 90.00
Int Tables number	5
Space group name H-M	C121
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-567- HOH
2	1	A-860- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Psilocybin synthase / Psilocybin biosynthesis methyltransferase Mass: 35889.578 Da / Num. of mol.: 2 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

#1: Protein

Psilocybin synthase / Psilocybin biosynthesis methyltransferase

Mass: 35889.578 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 722 molecules

#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-XP6 / Norbaeocystin / [3-(2-azanylethyl)-1~{H}-indol-4-yl] dihydrogen phosphate Mass: 256.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₂O₄P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.8 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris/HCl pH 8.5, 20% PEG 8000, 200 mM MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.6888 Å
Detector	Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 4, 2023 / Details: Toroidal mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6888 Å / Relative weight: 1
Reflection	Resolution: 1.18→20.69 Å / Num. obs: 225046 / % possible obs: 97.21 % / Redundancy: 14.1 % / B_iso Wilson estimate: 16.7 Å² / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.1241 / R_pim(I) all: 0.03473 / R_rim(I) all: 0.1289 / Net I/σ(I): 8.25
Reflection shell	Resolution: 1.18→1.222 Å / Redundancy: 14.5 % / R_merge(I) obs: 2.954 / Mean I/σ(I) obs: 0.31 / Num. unique obs: 19200 / CC_1/2: 0.374 / CC star: 0.738 / R_pim(I) all: 0.797 / R_rim(I) all: 3.06 / % possible all: 84.57

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
xia2	3.12.0	data reduction
xia2	3.12.0	data scaling
PHASER	2.8.2	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.18→20.69 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1961	3287	1.48 %
R_work	0.1833	-	-
obs	0.1835	221608	97.18 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 23.88 Å²

Refinement step

Cycle: LAST / Resolution: 1.18→20.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4845	0	91	713	5649

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	5215
X-RAY DIFFRACTION	f_angle_d	1.306	7122
X-RAY DIFFRACTION	f_dihedral_angle_d	13.738	1964
X-RAY DIFFRACTION	f_chiral_restr	0.094	787
X-RAY DIFFRACTION	f_plane_restr	0.016	938

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.18-1.2	0.376	119	0.388	7682	X-RAY DIFFRACTION	79
1.2-1.22	0.3524	113	0.3666	8388	X-RAY DIFFRACTION	86
1.22-1.24	0.3542	152	0.364	9200	X-RAY DIFFRACTION	95
1.24-1.26	0.352	164	0.3514	9443	X-RAY DIFFRACTION	97
1.26-1.28	0.3444	110	0.3535	9506	X-RAY DIFFRACTION	98
1.28-1.3	0.3529	147	0.345	9541	X-RAY DIFFRACTION	98
1.3-1.33	0.3417	143	0.3126	9558	X-RAY DIFFRACTION	98
1.33-1.36	0.3035	153	0.293	9540	X-RAY DIFFRACTION	98
1.36-1.39	0.3013	136	0.2626	9607	X-RAY DIFFRACTION	98
1.39-1.43	0.261	146	0.2381	9551	X-RAY DIFFRACTION	99
1.43-1.47	0.2195	153	0.2175	9580	X-RAY DIFFRACTION	99
1.47-1.51	0.2389	122	0.2016	9636	X-RAY DIFFRACTION	99
1.51-1.56	0.2123	164	0.1952	9641	X-RAY DIFFRACTION	99
1.56-1.61	0.2012	143	0.1842	9627	X-RAY DIFFRACTION	99
1.61-1.68	0.2139	148	0.1705	9678	X-RAY DIFFRACTION	99
1.68-1.75	0.2274	145	0.1646	9650	X-RAY DIFFRACTION	99
1.75-1.85	0.1471	146	0.1634	9697	X-RAY DIFFRACTION	99
1.85-1.96	0.1952	145	0.1711	9725	X-RAY DIFFRACTION	99
1.96-2.11	0.1624	147	0.1598	9731	X-RAY DIFFRACTION	99
2.11-2.33	0.1979	148	0.1569	9743	X-RAY DIFFRACTION	99
2.33-2.66	0.1965	156	0.1626	9752	X-RAY DIFFRACTION	99
2.66-3.35	0.1675	143	0.1701	9878	X-RAY DIFFRACTION	100
3.35-20.69	0.157	144	0.1608	9967	X-RAY DIFFRACTION	99

Refinement TLS params.

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

ID	L11 (°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)
1	0.3207	0.1075	0.1186	0.1577	-0.0086	0.1417	0.0044	0.3201	0.1167	-0.0989	-0.0067	0.0769	-0.0416	-0.0267	-0	0.1727	0.0198	0.0036	0.256	0.0268	0.1887	-34.0856	12.083	26.7262
2	0.8434	-0.0733	-0.1774	0.6223	-0.0556	0.5199	-0.0104	-0.002	-0.0518	0.0042	0.0015	0.0169	0.0132	-0.0328	0	0.1354	0.0055	0.0053	0.1367	0.0033	0.1604	-18.7181	5.4499	39.9407
3	0.6681	0.1685	-0.189	0.6298	0.2288	0.2921	0.0193	0.0819	0.0522	-0.1029	-0.0146	-0.1915	-0.0472	0.0235	-0.0009	0.1461	0.0108	0.0192	0.1624	0.0132	0.2	-5.068	8.0469	35.4425
4	0.0345	-0.0142	-0.0154	0.022	0.0109	0.0246	-0.1632	0.2342	0.0149	-0.3992	0.1723	-0.0862	-0.2206	0.2048	0.0002	0.3598	-0.0249	0.0652	0.3463	-0.005	0.2732	-2.7288	7.4028	20.8611
5	0.033	0.0101	-0.0187	0.1035	-0.0161	0.2084	0.0834	-0.4672	-0.0664	0.2313	-0.0928	0.0613	0.1534	-0.2545	0.0039	0.2082	-0.0082	0.0199	0.3285	-0.0229	0.1923	-10.4055	-1.9348	95.1038
6	0.365	-0.1549	0.0501	0.1637	-0.0495	0.2904	-0.0485	-0.0924	-0.0867	0.0827	0.0733	0.0097	0.0192	-0.0268	0.0009	0.191	-0.0028	0.0129	0.1885	0.0022	0.1602	-9.7989	-3.8853	85.0348
7	0.1095	-0.0367	-0.0606	0.025	0.021	0.0452	0.0369	-0.0236	-0.1147	0.0849	0.011	0.041	0.1227	0.0589	0.0128	0.2144	-0	-0.0112	0.1423	-0.004	0.1979	-9.9533	-16.0163	73.4363
8	0.5598	0.0116	-0.0243	0.1659	0.2977	0.7953	0.0033	0.0199	-0.0384	0.0276	-0.0073	-0.0064	0.0422	0.1104	0	0.1528	-0.001	-0.0071	0.1402	0.0006	0.1553	-5.2387	-7.0901	70.0373
9	0.0163	0.0143	0.0009	0.0147	-0.0031	0.0062	-0.0566	-0.1074	0.2206	0.007	0.1648	0.0729	-0.1005	-0.0245	-0	0.2862	0.0456	-0.0023	0.2288	-0.0084	0.2469	-14.3462	11.245	80.711
10	0.1526	-0.0783	-0.0749	0.0519	0.0638	0.0899	-0.1232	0.089	0.0548	-0.16	0.0583	0.1203	-0.2018	0.0401	0	0.1885	-0.0168	-0.023	0.1752	0.0063	0.1649	-12.8337	1.9543	63.4589
11	0.2332	0.0779	0.0754	0.2539	-0.1393	0.1427	-0.0127	-0.0554	-0.0245	0.0131	-0.0212	0.2644	0.0514	-0.1891	-0	0.1865	-0.0191	-0.0174	0.2091	-0.0184	0.2257	-23.2454	-5.9226	65.3261
12	0.132	-0.0219	-0.0037	0.1554	-0.16	0.1694	-0.0223	-0.1294	-0.0073	0.2079	-0.0476	0.2588	0.0141	-0.2125	-0	0.2078	-0.0225	0.027	0.2395	-0.0172	0.2384	-24.0307	-6.6824	72.4357
13	0.0497	0.0607	0.1239	0.0768	0.1567	0.3394	0.0505	-0.1187	-0.0296	0.1169	-0.0858	0.1236	0.0932	-0.3079	0.0099	0.251	0.0096	0.096	0.4709	-0.0574	0.4578	-32.9755	-4.7151	73.6391
14	0.1806	0.0122	0.232	0.0118	0.0026	0.3135	0.043	0.0169	-0.122	0.0469	0.0399	0.0091	0.0111	-0.0193	0.0006	0.1706	0.0075	-0.0107	0.1652	0.0062	0.1822	-16.531	13.0086	43.5713
15	0.0012	0.009	-0.0027	0.1396	-0.0229	0.0061	0.0226	-0.0244	-0.0334	0.0604	0.0644	-0.0679	-0.0169	0.078	0.0004	0.1857	0.0057	0.0048	0.2093	0.0177	0.2195	-18.3837	17.934	34.8778
16	0.0202	0.0017	-0.0958	0.0141	-0.0088	0.4555	-0.084	0.0089	-0.0181	0.0224	0.0397	0.0268	-0.0252	-0.0003	-0.0002	0.1857	-0.0142	0.0028	0.178	-0.0143	0.1754	-6.8474	0.6726	69.7434
17	0.0064	-0.0237	0.0239	0.6503	0.1353	0.1787	-0.019	0.0167	-0.0124	0.0044	0.0331	-0.0359	0.0585	-0.0139	-0.0023	0.2158	-0.0009	-0.0179	0.2105	0	0.2027	-12.3448	5.5994	76.7413

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 57 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 58 through 210 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 211 through 294 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 295 through 309 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 29 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 30 through 93 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 94 through 112 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 113 through 195 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 196 through 210 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 211 through 236 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 237 through 274 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 275 through 294 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 295 through 309 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 401 through 401)
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 501 through 501)
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 401 through 401)
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 501 through 501)

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