PDB-9dgd: Tetrahydroprotoberberine N-methyltransferase in complex with bold...

ID or keywords:

Entry

Database: PDB / ID: 9dgd

Title

Tetrahydroprotoberberine N-methyltransferase in complex with boldine and SAH

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 / Boldine / S-ADENOSYL-L-HOMOCYSTEINE / Tetrahydroprotoberberine N-methyltransferase

Function and homology information

Biological species

Glaucium flavum (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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	9dgd.cif.gz	100.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9dgd.ent.gz	71.1 KB	Display	PDB format
PDBx/mmJSON format	9dgd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dgd_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9dgd_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9dgd_validation.xml.gz	23.2 KB	Display
Data in CIF	9dgd_validation.cif.gz	32.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dg/9dgd ftp://data.pdbj.org/pub/pdb/validation_reports/dg/9dgd	HTTPS FTP

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Related structure data

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

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

Unit cell

Length a, b, c (Å)	104.020, 104.020, 82.597
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-686- 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GHT / Boldine Mass: 325.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₉NO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / 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: 58.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 26% pentaerythritol ethoxylate, 15 mM ammonium sulfate, 0.1M Tris-Cl, 0.5 mM boldine, 0.5 mM SAM, 5% glycerol

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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: 1.8→39.544 Å / Num. obs: 48088 / % possible obs: 99.91 % / Redundancy: 12.9 % / CC_1/2: 1 / R_sym value: 0.016 / Net I/σ(I): 14.84
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 1.14 / Num. unique obs: 2661 / CC_1/2: 0.697 / R_sym value: 0.437 / % possible all: 100

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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: 1.8→39.544 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.959 / SU B: 1.845 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.091 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1869	2460	5.116 %	RANDOM
R_work	0.1681	45628	-	-
all	0.169	-	-	-
obs	-	48088	99.917 %	-

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: 36.251 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.114 Å²	0.057 Å²	-0 Å²
2-	-	0.114 Å²	0 Å²
3-	-	-	-0.37 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→39.544 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2697	0	50	358	3105

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2971
X-RAY DIFFRACTION	r_angle_refined_deg	1.416	1.852	4028
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.959	5	361
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.153	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.665	10	549
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.321	10	141
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	427
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2277
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	1517
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	2030
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	306
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.195	0.2	70
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.229	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	4.742	4.18	1411
X-RAY DIFFRACTION	r_mcangle_it	5.582	6.961	1783
X-RAY DIFFRACTION	r_scbond_it	7.139	4.991	1560
X-RAY DIFFRACTION	r_scangle_it	9.544	8.264	2245
X-RAY DIFFRACTION	r_lrange_it	11.19	39.498	4997

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
1.8-1.847	0.221	164	0.21	3357	0.211	3521	0.969	0.973	100	0.21
1.847-1.897	0.228	156	0.205	3264	0.206	3421	0.964	0.973	99.9708	0.205
1.897-1.952	0.221	188	0.189	3137	0.191	3326	0.968	0.976	99.9699	0.189
1.952-2.012	0.19	176	0.186	3072	0.186	3250	0.976	0.978	99.9385	0.186
2.012-2.078	0.205	169	0.19	2972	0.191	3144	0.973	0.977	99.9046	0.19
2.078-2.15	0.224	169	0.183	2864	0.186	3034	0.968	0.979	99.967	0.183
2.15-2.231	0.203	156	0.173	2779	0.175	2936	0.975	0.982	99.9659	0.173
2.231-2.322	0.174	160	0.172	2664	0.172	2825	0.98	0.982	99.9646	0.172
2.322-2.425	0.204	137	0.174	2596	0.175	2736	0.971	0.981	99.8904	0.174
2.425-2.543	0.203	124	0.165	2487	0.167	2614	0.976	0.983	99.8852	0.165
2.543-2.68	0.182	115	0.168	2351	0.169	2466	0.98	0.982	100	0.168
2.68-2.842	0.218	130	0.17	2232	0.172	2363	0.97	0.982	99.9577	0.17
2.842-3.037	0.184	100	0.161	2108	0.162	2211	0.979	0.984	99.8643	0.161
3.037-3.278	0.204	116	0.161	1944	0.164	2065	0.975	0.984	99.7579	0.161
3.278-3.589	0.152	93	0.157	1836	0.156	1929	0.986	0.985	100	0.157
3.589-4.008	0.157	91	0.143	1642	0.144	1734	0.986	0.987	99.9423	0.143
4.008-4.621	0.152	72	0.137	1465	0.138	1542	0.986	0.989	99.6757	0.137
4.621-5.64	0.155	66	0.163	1248	0.163	1316	0.983	0.984	99.848	0.163
5.64-7.896	0.197	46	0.2	1008	0.2	1054	0.967	0.974	100	0.2
7.896-39.544	0.234	32	0.199	600	0.2	633	0.96	0.974	99.842	0.199

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