PDB-6gkz: Crystal structure of Coclaurine N-Methyltransferase (CNMT) bound ...

ID or keywords:

Entry

Database: PDB / ID: 6gkz

Title

Crystal structure of Coclaurine N-Methyltransferase (CNMT) bound to N-methylheliamine and SAH

Components

Coclaurine N-methyltransferase

Keywords

TRANSFERASE / N-methylheliamine / Coclaurine N-Methyltransferase

Function / homology

(RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase / (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase activity / Mycolic acid cyclopropane synthetase / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / cytoplasm / S-ADENOSYL-L-HOMOCYSTEINE / Coclaurine N-methyltransferase

Function and homology information

Biological species

Coptis japonica (Japanese goldthread)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.43 Å

Authors

Dunstan, M.S. / Levy, C.W.

Funding support

United Kingdom, 1items

Citation

Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Structure and Biocatalytic Scope of Coclaurine N-Methyltransferase.
Authors: Bennett, M.R. / Thompson, M.L. / Shepherd, S.A. / Dunstan, M.S. / Herbert, A.J. / Smith, D.R.M. / Cronin, V.A. / Menon, B.R.K. / Levy, C. / Micklefield, J.

History

Deposition	May 22, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 2.0	Oct 23, 2024	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6gkz.cif.gz	564.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6gkz.ent.gz	466.4 KB	Display	PDB format
PDBx/mmJSON format	6gkz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/6gkz ftp://data.pdbj.org/pub/pdb/validation_reports/gk/6gkz	HTTPS FTP

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Related structure data

Related structure data	6gkvC 6gkyC C: citing same article (ref.)
Similar structure data	6gkv-d 5koc-d 6p3m-1 6p3o-1 5kpc-d 6p3n-1 3w8l-d 1v3d-d 6bw3-d 5xwr-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Coclaurine N-methyltransferase

B: Coclaurine N-methyltransferase

C: Coclaurine N-methyltransferase

D: Coclaurine N-methyltransferase

hetero molecules

168 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Coclaurine N-methyltransferase

D: Coclaurine N-methyltransferase

hetero molecules

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

2

C: Coclaurine N-methyltransferase

hetero molecules

B: Coclaurine N-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	141.750, 203.430, 54.540
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Coclaurine N-methyltransferase Mass: 41586.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coptis japonica (Japanese goldthread) / Gene: cnmt / Production host: Escherichia coli (E. coli) References: UniProt: Q948P7, (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 49.77 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.12 M Ethylene Glycol 0.1 M HEPES/MOPS (pH 7.4) 37.5 % MPD_PEG 1K/PEG 3350 and 1 mM AdoHcy

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 28, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→66.929 Å / Num. obs: 60299 / % possible obs: 99.7 % / Redundancy: 18.4 % / Net I/σ(I): 17.7
Reflection shell	Resolution: 2.4→2.48 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.24	data extraction
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.43→66.929 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.02

	R_factor	Num. reflection	% reflection
R_free	0.2427	3081	5.11 %
R_work	0.1645	-	-
obs	0.1684	60299	99.62 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 177.42 Å² / B_iso mean: 39.1761 Å² / B_iso min: 13.16 Å²

Refinement step

Cycle: final / Resolution: 2.43→66.929 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11009	0	172	325	11506
B_iso mean	-	-	62.4	38.81	-
Num. residues	-	-	-	-	1346

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11445
X-RAY DIFFRACTION	f_angle_d	1.097	15465
X-RAY DIFFRACTION	f_chiral_restr	0.042	1700
X-RAY DIFFRACTION	f_plane_restr	0.004	1950
X-RAY DIFFRACTION	f_dihedral_angle_d	16.38	4232

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.43-2.468	0.3124	136	0.1972	2567	2703	100
2.468-2.5085	0.301	138	0.1891	2529	2667	98
2.5085-2.5517	0.3026	145	0.1901	2556	2701	100
2.5517-2.5981	0.3105	130	0.1916	2586	2716	99
2.5981-2.6481	0.3042	145	0.1932	2505	2650	100
2.6481-2.7022	0.2612	120	0.1931	2623	2743	100
2.7022-2.7609	0.2696	138	0.1947	2553	2691	99
2.7609-2.8251	0.3172	151	0.1915	2552	2703	100
2.8251-2.8958	0.269	131	0.1844	2589	2720	99
2.8958-2.9741	0.2713	145	0.1818	2563	2708	100
2.9741-3.0616	0.2919	152	0.1834	2573	2725	99
3.0616-3.1604	0.262	143	0.1854	2574	2717	100
3.1604-3.2734	0.2756	128	0.1754	2577	2705	100
3.2734-3.4044	0.257	155	0.1733	2609	2764	100
3.4044-3.5594	0.2462	146	0.1722	2585	2731	100
3.5594-3.747	0.2268	136	0.1557	2599	2735	100
3.747-3.9817	0.2072	127	0.144	2641	2768	100
3.9817-4.2891	0.2	132	0.1327	2633	2765	100
4.2891-4.7206	0.1712	150	0.1239	2634	2784	100
4.7206-5.4035	0.197	140	0.1417	2677	2817	100
5.4035-6.8068	0.2561	157	0.181	2678	2835	100
6.8068-66.9547	0.2156	136	0.1579	2815	2951	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	0.8809	0.5346	-0.0055	1.6389	0.0767	0.6721	0.0573	-0.1372	0.1046	0.215	-0.1232	-0.0753	-0.3425	-0.0092	0.0279	0.3361	-0.0625	-0.0241	0.2024	-0.0246	0.1805	133.737	44.5034	45.4338
2	1.0275	0.2192	0.1396	0.7037	-0.573	0.3066	0.0706	-0.1148	0.119	-0.0501	-0.1296	-0.0805	-0.3439	0.1872	-0.0142	0.2287	-0.055	-0.0123	0.2572	0.0264	0.1787	141.2106	37.9798	20.6337
3	0.8452	-0.4844	0.0214	0.8442	-0.3679	1.1047	0.0252	0.1638	0.0233	-0.0795	-0.0528	-0.0144	-0.1506	-0.0695	0.0019	0.1711	-0.0515	-0.0083	0.2355	0.0005	0.1688	132.0836	35.0431	13.7595
4	0.6836	0.2077	-0.1885	1.1508	0.1115	1.4763	0.0122	-0.0229	0.1341	0.1691	-0.0377	0.001	-0.3275	0.0735	-0.0043	0.249	-0.0423	-0.0517	0.2002	0.0308	0.2207	137.8371	43.2968	32.804
5	0.522	-0.8284	0.6713	2.452	-1.7199	1.1828	-0.124	-0.0278	-0.1918	0.0484	-0.3365	-0.9882	0.0406	0.4016	0.0695	0.2881	0.0031	-0.0485	0.3658	0.1092	0.556	193.1175	25.0593	26.3568
6	0.6221	0.4708	0.1905	1.306	-0.6701	0.5804	0.0384	-0.0439	-0.1624	-0.0817	-0.0131	-0.2141	0.0777	-0.0276	0.0846	0.2139	-0.0057	0.0355	0.2294	0.0043	0.2782	170.1874	24.5699	14.5271
7	1.4504	0.6409	-0.159	1.6378	-0.0655	0.838	-0.023	0.0453	-0.202	-0.3087	-0.0017	-0.1342	0.166	-0.0528	0.0717	0.3167	-0.0366	-0.0069	0.2524	0.015	0.26	163.6895	15.9559	6.2513
8	0.8109	-0.0316	0.4403	1.1056	-0.2989	0.8949	-0.0139	-0.084	-0.1515	0.0495	-0.0783	-0.2914	0.0174	0.1634	0.0526	0.2202	-0.0065	0.0152	0.2421	0.0448	0.3366	178.867	23.4506	19.1312
9	0.7208	-0.3079	-0.1376	2.5428	0.0986	0.7467	-0.0213	0.0144	-0.0296	-0.4344	0.0653	0.0843	-0.0359	-0.0646	0.0049	0.1683	-0.0096	-0.0279	0.2025	0.0014	0.1846	98.3769	39.4489	37.7638
10	1.8838	-2.3119	0.4834	3.1198	-0.5003	0.3611	0.2965	-0.0783	-0.1076	0.0299	0.0483	0.4001	0.1501	-0.2141	-0.0957	0.3744	-0.0471	0.0467	0.3632	0.0399	0.2862	96.5617	36.1798	59.0014
11	1.4347	-1.224	-0.6446	2.7127	1.1107	2.4691	-0.045	0.0063	-0.0627	0.2537	0.045	-0.137	-0.2259	0.0682	-0.061	0.2808	0.0178	-0.0555	0.231	0.0259	0.1673	111.4034	43.5225	64.0062
12	1.5554	0.0729	0.6074	1.7282	-0.7076	2.1294	-0.0912	-0.0475	-0.0124	0.202	0.0541	0.1321	-0.0652	-0.4203	-0.0176	0.3303	0.0862	0.0547	0.355	0.0273	0.2016	100.8631	41.02	74.5984
13	0.448	-0.5564	0.2111	1.455	-0.1354	1.022	-0.0166	0.0113	-0.0671	0.0677	-0.0013	0.1657	-0.0616	-0.0594	-0.0173	0.2028	0.0198	0.031	0.2067	0.0148	0.2051	100.6189	41.2779	52.9054
14	0.6083	-0.0638	0.1039	0.811	-0.1689	1.1965	-0.0085	-0.0067	-0.0643	0.1386	-0.1108	-0.2246	0.0075	0.3477	0.0688	0.1372	-0.0223	-0.0323	0.2407	0.0525	0.2495	144.7539	7.9727	50.6482
15	0.2266	0.0805	-0.164	0.5642	-0.5062	1.3344	0.0142	-0.0391	-0.2289	-0.0605	0.0103	-0.1368	0.0161	-0.2243	0.081	0.1916	-0.0857	-0.0242	0.256	-0.0225	0.3381	124.0333	1.9998	51.0495
16	0.6548	0.5643	0.2854	0.5161	0.5796	2.8541	0.0104	-0.084	-0.1091	0.1921	0.0749	0.287	0.1568	-0.2876	0.0058	0.2061	-0.0275	0.0278	0.1983	-0.0078	0.1968	113.6314	7.19	46.3307
17	1.1931	0.4449	-0.0245	1.3642	-0.4435	0.5209	-0.1206	-0.0124	-0.1866	-0.102	0.1164	-0.0241	0.0584	-0.0227	0.0367	0.2081	-0.0318	0.0186	0.2272	-0.0011	0.2443	114.9053	-2.1312	39.7599
18	0.7833	0.0594	0.1368	0.7201	-0.0675	0.6748	-0.0157	0.073	-0.0954	-0.0687	-0.0143	-0.1039	0.0508	0.0701	0.0091	0.1666	0.0031	0.0073	0.1988	0.0154	0.1673	131.2668	8.9234	39.2114
19	1.4457	-0.3625	-0.1536	1.9654	-0.9386	1.1842	-0.0127	-0.2799	-0.3765	0.0523	-0.0486	-0.2338	0.1562	0.0333	0.038	0.208	-0.0243	-0.028	0.2078	0.0574	0.2723	130.4982	-5.8175	61.053
20	2.6518	-0.1451	2.0411	0.5813	0.0645	1.9497	-0.2975	-0.4463	-0.039	0.2386	0.2499	-0.0559	-0.4839	-0.2595	0.0277	0.239	-0.0304	-0.0303	0.2609	0.0345	0.2027	131.0987	13.7893	49.8902

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 64 )	A	7 - 64
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 65 through 141 )	A	65 - 141
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 142 through 233 )	A	142 - 233
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 234 through 356 )	A	234 - 356
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 45 )	B	8 - 45
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 46 through 141 )	B	46 - 141
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 142 through 233 )	B	142 - 233
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 234 through 357 )	B	234 - 357
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 9 through 64 )	C	9 - 64
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 65 through 94 )	C	65 - 94
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 95 through 141 )	C	95 - 141
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 142 through 198 )	C	142 - 198
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 199 through 357 )	C	199 - 357
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 10 through 64 )	D	10 - 64
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 65 through 109 )	D	65 - 109
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 110 through 141 )	D	110 - 141
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 142 through 211 )	D	142 - 211
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 212 through 286 )	D	212 - 286
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 287 through 335 )	D	287 - 335
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 336 through 356 )	D	336 - 356

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