PDB-9dga: Tetrahydroprotoberberine N-methyltransferase in complex with (R)-...

ID or keywords:

Entry

Database: PDB / ID: 9dga

Title

Tetrahydroprotoberberine N-methyltransferase in complex with (R)-reticuline and SAM

Components

Tetrahydroprotoberberine N-methyltransferase

Keywords

TRANSFERASE / methyltransferase / benzylisoquinoline alkaloid

Function / homology

(S)-tetrahydroprotoberberine N-methyltransferase / (S)-tetrahydroprotoberberine N-methyltransferase activity / Mycolic acid cyclopropane synthetase / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / : / S-ADENOSYLMETHIONINE / Tetrahydroprotoberberine N-methyltransferase

Function and homology information

Biological species

Glaucium flavum (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Lang, D.E. / Ng, K.K.S.

Funding support

Canada, 1items

Citation

Journal: To Be Published
Title: The stereospecific activities of the tetrahydroprotoberberine N-methyltransferase with alternative substrates provide insight into the catalytic mechanisms of benzylisoquinoline alkaloid N-methylation.
Authors: Lang, D.E. / Ng, K.K.S. / Rehman, F. / Morris, J.S. / Facchini, P.J.

History

Deposition	Sep 2, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dga.cif.gz	102.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9dga.ent.gz		Display	PDB format
PDBx/mmJSON format	9dga.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dga_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	9dga_full_validation.pdf.gz	1.6 MB	Display
Data in XML	9dga_validation.xml.gz	22.6 KB	Display
Data in CIF	9dga_validation.cif.gz	32.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dg/9dga ftp://data.pdbj.org/pub/pdb/validation_reports/dg/9dga	HTTPS FTP

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Related structure data

Related structure data	9dg6C 9dg7C 9dg8C 9dg9C 9dgbC 9dgcC 9dgdC 9dgeC 9dgfC 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
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Tetrahydroprotoberberine N-methyltransferase

hetero molecules

44.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tetrahydroprotoberberine N-methyltransferase

hetero molecules

A: Tetrahydroprotoberberine N-methyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
89.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.013, 104.013, 82.863
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Tetrahydroprotoberberine N-methyltransferase Mass: 43801.926 Da / Num. of mol.: 1 / Mutation: E204A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glaucium flavum (plant) / Production host: Escherichia coli (E. coli) References: UniProt: A0A5S8WF76, (S)-tetrahydroprotoberberine N-methyltransferase
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1A4H / (R)-reticuline / (1R)-1-[(3-hydroxy-4-methoxyphenyl)methyl]-6-methoxy-2-methyl-1,2,3,4-tetrahydroisoquinolin-7-ol Mass: 329.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₂₃NO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 58.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Tris-Cl, 15 mM ammonium sulfate, 29% pentaerythritol ethoxylate (15/4 EO/OH), 5% glycerol, 0.5 mM SAM, 0.5 mM R-reticuline

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2→37.641 Å / Num. obs: 34747 / % possible obs: 98.36 % / Redundancy: 3.4 % / CC_1/2: 0.996 / R_sym value: 0.044 / Net I/σ(I): 10.31
Reflection shell	Resolution: 2→2.05 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 4.78 / Num. unique obs: 2673 / CC_1/2: 0.939 / R_sym value: 0.139 / % possible all: 99.81

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→37.641 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.943 / WR_factor R_free: 0.191 / WR_factor R_work: 0.146 / SU B: 2.58 / SU ML: 0.072 / Average fsc free: 0.9751 / Average fsc work: 0.985 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.123 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1906	1783	5.131 %	RANDOM
R_work	0.1463	32964	-	-
all	0.149	-	-	-
obs	-	34747	98.344 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 28.469 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.061 Å²	0.031 Å²	0 Å²
2-	-	0.061 Å²	-0 Å²
3-	-	-	-0.198 Å²

Refinement step

Cycle: LAST / Resolution: 2→37.641 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2696	0	51	390	3137

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2967
X-RAY DIFFRACTION	r_angle_refined_deg	1.379	1.856	4018
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.923	5	357
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.166	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.282	10	541
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.291	10	138
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	425
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2260
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	1479
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	2010
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.208	0.2	357
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.21	0.2	74
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.197	0.2	43
X-RAY DIFFRACTION	r_mcbond_it	4.618	3.002	1401
X-RAY DIFFRACTION	r_mcangle_it	5.73	4.975	1767
X-RAY DIFFRACTION	r_scbond_it	7.512	4.002	1566
X-RAY DIFFRACTION	r_scangle_it	10.46	6.457	2251
X-RAY DIFFRACTION	r_lrange_it	14.003	30.859	4999

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2-2.052	0.23	110	0.187	2463	0.189	2578	0.964	0.977	99.8061	0.187
2.052-2.108	0.223	142	0.172	2365	0.175	2515	0.968	0.981	99.6819	0.172
2.108-2.169	0.209	129	0.172	2294	0.174	2442	0.972	0.98	99.222	0.172
2.169-2.236	0.193	119	0.156	2221	0.158	2353	0.977	0.985	99.4475	0.156
2.236-2.309	0.195	114	0.153	2218	0.155	2338	0.975	0.986	99.7434	0.153
2.309-2.389	0.194	107	0.15	2081	0.152	2207	0.977	0.986	99.1391	0.15
2.389-2.479	0.195	109	0.147	2044	0.149	2165	0.979	0.986	99.4457	0.147
2.479-2.58	0.203	115	0.143	1953	0.146	2071	0.973	0.987	99.8551	0.143
2.58-2.694	0.242	109	0.157	1886	0.161	1995	0.964	0.984	100	0.157
2.694-2.825	0.212	96	0.158	1812	0.16	1917	0.97	0.984	99.5305	0.158
2.825-2.977	0.206	89	0.144	1708	0.147	1811	0.977	0.987	99.2269	0.144
2.977-3.156	0.171	92	0.145	1599	0.146	1739	0.982	0.987	97.2398	0.145
3.156-3.372	0.159	80	0.141	1490	0.142	1622	0.983	0.988	96.7941	0.141
3.372-3.64	0.216	91	0.127	1363	0.131	1503	0.972	0.99	96.7399	0.127
3.64-3.984	0.151	68	0.122	1315	0.124	1424	0.988	0.991	97.1208	0.122
3.984-4.448	0.129	67	0.118	1158	0.118	1271	0.991	0.991	96.3808	0.118
4.448-5.124	0.157	47	0.123	1046	0.124	1148	0.983	0.991	95.2091	0.123
5.124-6.246	0.22	52	0.161	847	0.164	969	0.975	0.984	92.7761	0.161
6.246-8.715	0.168	28	0.165	694	0.165	779	0.985	0.983	92.6829	0.165
8.715-37.641	0.233	19	0.172	405	0.175	475	0.964	0.978	89.2632	0.172

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