PDB-9dge: Tetrahydroprotoberberine N-methyltransferase product complex with...

ID or keywords:

Entry

Database: PDB / ID: 9dge

Title

Tetrahydroprotoberberine N-methyltransferase product complex with dextromethorphan 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: 1.6 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	9dge.cif.gz	102.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9dge.ent.gz	72.9 KB	Display	PDB format
PDBx/mmJSON format	9dge.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dge_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9dge_full_validation.pdf.gz	1.2 MB	Display
Data in XML	9dge_validation.xml.gz	21.4 KB	Display
Data in CIF	9dge_validation.cif.gz	30.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dg/9dge ftp://data.pdbj.org/pub/pdb/validation_reports/dg/9dge	HTTPS FTP

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Related structure data

Related structure data	9dg6C 9dg7C 9dg8C 9dg9C 9dgaC 9dgbC 9dgcC 9dgdC 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

44.6 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)	103.992, 103.992, 82.536
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

Components on special symmetry positions

ID	Model	Components
1	1	A-741- HOH
2	1	A-746- HOH

#1: Protein	Tetrahydroprotoberberine N-methyltransferase Mass: 43801.926 Da / Num. of mol.: 1 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-4NQ / 3-methoxy-17-methyl-9alpha,13alpha,14alpha-morphinan Mass: 271.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₈H₂₅NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.94 Å³/Da / Density % sol: 58.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 26% pentaerythritol ethoxylate (15/4 EO/OH), 0.1 M Tris-Cl, 10 mM ammonium sulfate, 5% glycerol, 0.5 mM dextromethorphan, 0.5 mM SAM

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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: Nov 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: 1.6→39.53 Å / Num. obs: 68044 / % possible obs: 99.88 % / Redundancy: 13.4 % / CC_1/2: 1 / R_sym value: 0.011 / Net I/σ(I): 19.52
Reflection shell	Resolution: 1.6→1.62 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.98 / Num. unique obs: 2684 / CC_1/2: 0.791 / R_sym value: 0.312 / % possible all: 99.7

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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: 1.6→39.53 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.966 / SU B: 1.316 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.071 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.1912	3480	5.114 %
R_work	0.1707	64563	-
all	0.172	-	-
obs	-	68043	99.877 %

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: 38.517 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.088 Å²	0.044 Å²	0 Å²
2-	-	0.088 Å²	-0 Å²
3-	-	-	-0.285 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→39.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2721	0	52	343	3116

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	3049
X-RAY DIFFRACTION	r_angle_refined_deg	1.117	1.836	4143
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.763	5	381
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	2.817	5	9
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.37	10	571
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.703	10	146
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	443
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2348
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	1444
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	2072
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	296
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.186	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	35
X-RAY DIFFRACTION	r_mcbond_it	3.578	4.495	1467
X-RAY DIFFRACTION	r_mcangle_it	5.059	7.494	1867
X-RAY DIFFRACTION	r_scbond_it	5.771	5.234	1582
X-RAY DIFFRACTION	r_scangle_it	8.356	8.733	2276
X-RAY DIFFRACTION	r_lrange_it	10.291	41.234	4944

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
1.6-1.642	0.279	239	0.244	4714	0.246	4961	0.945	0.959	99.8387	0.244
1.642-1.686	0.258	247	0.226	4604	0.228	4853	0.956	0.966	99.9588	0.226
1.686-1.735	0.233	246	0.207	4466	0.208	4724	0.963	0.972	99.746	0.207
1.735-1.788	0.202	248	0.194	4346	0.194	4594	0.974	0.977	100	0.194
1.788-1.847	0.217	247	0.188	4203	0.19	4454	0.97	0.978	99.9102	0.188
1.847-1.912	0.216	216	0.19	4095	0.192	4311	0.972	0.978	100	0.19
1.912-1.984	0.195	213	0.187	3962	0.188	4177	0.975	0.978	99.9521	0.187
1.984-2.064	0.208	212	0.185	3804	0.186	4016	0.974	0.979	100	0.185
2.064-2.156	0.198	211	0.186	3635	0.187	3847	0.973	0.978	99.974	0.186
2.156-2.261	0.18	187	0.177	3519	0.177	3714	0.981	0.981	99.7846	0.177
2.261-2.383	0.199	176	0.175	3310	0.177	3486	0.976	0.98	100	0.175
2.383-2.527	0.213	189	0.184	3157	0.185	3346	0.97	0.979	100	0.184
2.527-2.7	0.203	132	0.175	2999	0.176	3131	0.975	0.981	100	0.175
2.7-2.916	0.208	170	0.176	2768	0.177	2946	0.974	0.981	99.7284	0.176
2.916-3.192	0.191	127	0.166	2577	0.168	2704	0.978	0.983	100	0.166
3.192-3.566	0.164	114	0.152	2336	0.152	2450	0.985	0.986	100	0.152
3.566-4.112	0.153	104	0.139	2071	0.139	2190	0.983	0.988	99.3151	0.139
4.112-5.023	0.156	85	0.138	1767	0.138	1855	0.986	0.988	99.8383	0.138
5.023-7.047	0.206	80	0.186	1398	0.187	1478	0.976	0.978	100	0.186
7.047-39.53	0.174	37	0.179	832	0.179	884	0.98	0.977	98.3032	0.179

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