PDB-8xe4: norbelladine 4'-O-methyltransferase complexed with Mg, SAH, and n...

ID or keywords:

Entry

Database: PDB / ID: 8xe4

Title

norbelladine 4'-O-methyltransferase complexed with Mg, SAH, and norbelladine

Components

Norbelladine 4'-O-methyltransferase

Keywords

TRANSFERASE / O-methyltransferase family protein / NpN4OMT

Function / homology

Function and homology information

norbelladine O-methyltransferase / alkaloid metabolic process / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / metal ion binding
Similarity search - Function

Biological species

Narcissus pseudonarcissus MK-2014 (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.96 Å

Authors

Saw, Y.Y.H. / Nakashima, Y. / Morita, H.

Funding support

Japan, 2items

Citation

Journal: Acs Catalysis / Year: 2024
Title: Structure-Based Catalytic Mechanism of Amaryllidaceae O-Methyltransferases
Authors: Hnin, S.Y.Y. / Nakashima, Y. / Kodama, T. / Morita, H.

History

Deposition	Dec 11, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xe4.cif.gz	494 KB	Display	PDBx/mmCIF format
PDB format	pdb8xe4.ent.gz		Display	PDB format
PDBx/mmJSON format	8xe4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xe4_validation.pdf.gz	3.8 MB	Display	wwPDB validaton report
Full document	8xe4_full_validation.pdf.gz	3.8 MB	Display
Data in XML	8xe4_validation.xml.gz	45 KB	Display
Data in CIF	8xe4_validation.cif.gz	65.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xe/8xe4 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/8xe4	HTTPS FTP

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Related structure data

Related structure data	8xdoC 8xdpC 8xdqC 8xdrC 8xdsC 8xdtC 8xduC 8xdvC 8xdyC 8xe0C 8xe2C 8xe3C 8xe5C 8z8oC 8z8pC 8z8rC 8z8sC 8zfwC 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: Norbelladine 4'-O-methyltransferase

B: Norbelladine 4'-O-methyltransferase

C: Norbelladine 4'-O-methyltransferase

D: Norbelladine 4'-O-methyltransferase

hetero molecules

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

1

A: Norbelladine 4'-O-methyltransferase

hetero molecules

C: Norbelladine 4'-O-methyltransferase

hetero molecules

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

2

B: Norbelladine 4'-O-methyltransferase

D: Norbelladine 4'-O-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.728, 79.668, 92.009
Angle α, β, γ (deg.)	90.000, 93.852, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Norbelladine 4'-O-methyltransferase Mass: 27397.084 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Narcissus pseudonarcissus MK-2014 (plant) Gene: N4OMT / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A077EWA5

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Non-polymers , 5 types, 842 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-A1LU2 / Norbelladine Mass: 259.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₁₇NO₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 831 / 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: 2.16 Å³/Da / Density % sol: 43.05 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 15% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 8.0)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.04 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.04 Å / Relative weight: 1
Reflection	Resolution: 1.96→45.9 Å / Num. obs: 128044 / % possible obs: 99.6 % / Redundancy: 4.2 % / B_iso Wilson estimate: 17.4 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.139 / Net I/σ(I): 17.4
Reflection shell	Resolution: 1.96→2.01 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.669 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4478 / CC_1/2: 0.718 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.96→45.9 Å / SU ML: 0.1916 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 19.896
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.207	6544	5.11 %
R_work	0.17	121500	-
obs	0.1719	128044	97.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 22.46 Å²

Refinement step

Cycle: LAST / Resolution: 1.96→45.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7706	0	44	831	8581

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0038	8117
X-RAY DIFFRACTION	f_angle_d	0.7318	11069
X-RAY DIFFRACTION	f_chiral_restr	0.0481	1235
X-RAY DIFFRACTION	f_plane_restr	0.004	1415
X-RAY DIFFRACTION	f_dihedral_angle_d	20.3551	2989

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 (%)
1.96-1.98	0.2854	224	0.2498	4057	X-RAY DIFFRACTION	98.75
1.98-2.01	0.2757	239	0.2479	4122	X-RAY DIFFRACTION	98.78
2.01-2.03	0.2751	202	0.2425	4124	X-RAY DIFFRACTION	98.7
2.03-2.06	0.2905	218	0.2332	4104	X-RAY DIFFRACTION	98.52
2.06-2.08	0.2382	234	0.2248	4089	X-RAY DIFFRACTION	98.65
2.08-2.11	0.2737	255	0.2272	4086	X-RAY DIFFRACTION	98.86
2.11-2.14	0.2418	217	0.215	4169	X-RAY DIFFRACTION	98.34
2.14-2.17	0.2266	258	0.2096	4046	X-RAY DIFFRACTION	98.49
2.17-2.21	0.2569	220	0.2097	4043	X-RAY DIFFRACTION	98.27
2.21-2.24	0.2276	199	0.2034	4153	X-RAY DIFFRACTION	98.08
2.24-2.28	0.2445	231	0.1921	4049	X-RAY DIFFRACTION	98.35
2.28-2.32	0.2297	189	0.1903	4121	X-RAY DIFFRACTION	98.02
2.32-2.37	0.2098	211	0.189	4080	X-RAY DIFFRACTION	98.04
2.37-2.42	0.2332	219	0.1784	4079	X-RAY DIFFRACTION	97.44
2.42-2.47	0.2062	204	0.1803	3972	X-RAY DIFFRACTION	96.09
2.47-2.53	0.2116	204	0.1817	3962	X-RAY DIFFRACTION	94.62
2.53-2.59	0.2475	202	0.1775	3869	X-RAY DIFFRACTION	91.92
2.59-2.66	0.2178	220	0.1698	3814	X-RAY DIFFRACTION	92.74
2.66-2.74	0.2148	216	0.1677	4028	X-RAY DIFFRACTION	96.83
2.74-2.83	0.2245	213	0.1769	4157	X-RAY DIFFRACTION	98.65
2.83-2.93	0.2224	244	0.1704	4082	X-RAY DIFFRACTION	98.32
2.93-3.04	0.2165	202	0.1639	4057	X-RAY DIFFRACTION	98.11
3.04-3.18	0.1946	225	0.1612	4088	X-RAY DIFFRACTION	97.93
3.18-3.35	0.1918	233	0.1449	4049	X-RAY DIFFRACTION	98.12
3.35-3.56	0.1501	254	0.1363	4016	X-RAY DIFFRACTION	96.96
3.56-3.84	0.1644	217	0.1319	4050	X-RAY DIFFRACTION	96.78
3.84-4.22	0.1454	223	0.1237	3965	X-RAY DIFFRACTION	95.88
4.22-4.83	0.1435	193	0.1215	4034	X-RAY DIFFRACTION	96.13
4.83-6.09	0.2335	171	0.161	4067	X-RAY DIFFRACTION	96.23
6.09-45.9	0.1927	207	0.1586	3968	X-RAY DIFFRACTION	95.52

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	0.0160740103695	-0.0157074648074	0.0209312105222	0.0073092037725	-0.0247257292126	0.0289046989146	-0.012658699855	0.0515124741126	-0.0292589439755	0.00530277392806	0.0179303184182	-0.0514201089159	-0.015958428051	0.203691702524	-1.6993375987E-6	0.186413770368	0.0215537241438	0.0214696779142	0.193782560056	-0.00400185105888	0.165662838871	18.5553024155	6.69789483686	-4.25222468857
2	0.464427002154	0.113813923796	0.0969321781961	0.0925958396995	0.239557542218	0.433615002046	-0.00886126506736	-0.0674055164407	-0.052876395993	0.0569925026533	0.0170903092069	-0.0605636076611	-0.0365336572991	0.146678428976	-0.0595087008691	0.0503006201989	0.0278034019231	-0.0155397614062	0.108638098989	-0.0251265031959	0.0850480800653	23.5041110016	-8.07597399234	8.27089254215
3	0.139887567474	-0.163749138934	0.0138388723156	0.134861128329	0.0174266347857	0.10046432238	0.0137659350719	-0.00464403708016	0.0149024783467	-0.0190067287308	0.0207258733989	-0.0216001207377	0.0128697425092	0.0945639467132	0.0233898317834	0.111092546618	0.00613323713752	0.0114899290139	0.0597617525983	-0.0125940786889	0.0829971374807	12.8740107427	-9.41237717649	-6.29604359
4	0.0322914771651	-0.00386445020428	0.0135704107479	0.104935024531	0.0421585017847	0.142738998381	-0.0141484693509	-0.312830039256	0.292042973662	-0.0158270840756	-0.0553380748798	-0.197486233059	-0.208132317741	0.236224484619	-0.0203729430397	0.11059871601	-0.0420068596204	0.00138440344144	0.207940161588	-0.0381515897204	0.233626361487	43.595616399	9.49040727735	-32.2725721686
5	1.43761063276	-0.365798892873	-0.0332815026481	0.290001640364	0.128418260994	0.345524612818	-0.0793810000694	-0.275007153829	0.0383591801167	-0.0251005062396	0.0916975354694	-0.0960713313258	0.0121147862431	0.0282990594433	-0.0132609886987	0.053868681065	0.00338194171239	-0.0088908058892	0.110983832272	-0.015443103863	0.0795414006221	49.5742669176	-6.58314894856	-31.9684504473
6	0.110051385914	0.0148755808699	0.015096367772	0.041954638632	-0.00696444588877	0.0830994691464	-0.0590943097791	0.075435919109	0.0743527583855	-0.0401434048066	0.0249542154347	0.24013352924	-0.0861872299499	-0.11072501759	-0.0153255963777	0.0831183386292	0.0289703484388	0.0250907417146	0.0502818399308	-0.00440848426249	0.1109599773	57.43817316	-0.470792873362	1.6069430074
7	0.160757199545	0.0353132983128	-0.116929052825	0.217691983773	0.146691640689	0.33404385611	-0.00767437169245	-0.00396212139095	0.0508313477698	0.00406665955348	0.0370581345168	0.0579036175258	0.0202091951213	-0.0300894013264	0.0249432983482	0.105039125088	0.0114082430571	0.00860810102846	0.0725369378736	0.0181456906657	0.0879829623102	55.0850414533	-14.0594148291	8.37090388163
8	0.127072927877	-0.00728404122074	-0.0503771029794	0.0220708361117	-0.0155022931961	0.0638610115554	-0.0267908846613	-0.129761165415	-0.046065394586	-0.0417953093774	0.0594496557285	0.0506729933233	0.0807657955723	-0.0178861334434	-0.000119143428958	0.153881356932	0.017116196595	0.0247358363299	0.107306287903	0.0198546024291	0.120235450103	55.8554078226	-17.4268186825	22.2571884563
9	0.270545395737	0.0978417976553	-0.0983116984339	0.0992214042953	-0.0206067587086	0.110496918193	0.0305033453982	-0.130626691367	0.0670232260522	0.0273287830221	0.00516378475274	0.0187991943328	-0.0243778579259	0.0486888915025	0.0432201152757	0.126802500977	0.0279979782561	-0.00701687395552	0.0907995668496	-0.00913805748185	0.0600917928451	64.6678220564	-1.17254075067	20.0924991124
10	-0.000761881827328	-0.00620905567588	-0.000169839606826	0.0181685795966	0.0103957937371	-0.00207770540042	0.0717609651213	0.101778477736	-0.0392190393481	-0.0889131203277	0.155211174595	-0.110943997974	-0.0160131837519	-0.31145369785	0.000581863645223	0.176374890023	0.0586490663913	-0.00633025883474	0.293443219846	0.0692303253938	0.271522269988	24.5122079807	9.94933140183	-47.1400458297
11	0.139351752499	0.0594095283093	0.0438566432731	0.0351230883581	0.0358958361361	0.0130486360091	0.0580906723579	0.353395598198	0.130090275741	-0.0500455385804	0.0210135091824	-0.0263494694173	-0.0157626192075	-0.0181964559815	0.0146139338354	0.0923450384789	0.00438673050515	0.000475793777234	0.129278717176	0.0307002357649	0.091151645479	29.2813409103	-3.25968083326	-52.2853650985
12	0.0371524905383	0.0136376978134	-0.0194161806716	0.0162669072644	0.0195863173127	0.013780591924	0.0299862043408	-0.0564884380106	-0.0490489738392	0.00562763807745	0.0167348284495	-0.00455063006423	-0.0717802669559	0.00692876643178	0.00359349441434	0.0978222095492	-0.000588847656205	-0.00477696765677	0.08825841505	0.0146936092866	0.098922717844	28.2557746765	-12.4558579165	-37.6808767971
13	0.0997334455162	0.0230418814614	-0.077329060146	0.00540873409755	-0.0257962528613	0.0821753839585	-0.0611645491559	0.0645721860144	-0.098734829201	-0.0385236113501	0.0330991610796	0.0597787145765	0.0333946584068	-0.0305683285866	-0.0113569264622	0.0845022776436	-0.00577179493357	-0.0165215748078	0.089356423146	-0.00155647816006	0.0854384663424	18.209804016	-12.8280014571	-46.5102172855
14	0.0492971236188	-0.00922137725361	-0.00716550260224	0.143740630571	0.123300330351	0.134797629399	-0.00309823280509	-0.170651209886	-0.110053786406	-0.169598611596	-0.0370039299994	0.0325594006495	-0.0401596995021	-0.0643341740483	-0.0133764824828	0.0132938393519	0.00721336873355	0.00657291553624	0.0867206338592	0.0312263249773	0.117955321756	14.1867338887	-13.8134258074	-34.5240068388
15	0.35267275157	0.109099382564	-0.111960981142	0.0794705028857	0.0707364960755	0.113225122814	0.0141387153097	-0.153079367943	0.146808330757	-0.0129470142215	0.00337309188226	0.0558575186915	-0.0123564760065	-0.0416817529638	-0.00755186936209	0.073724783785	0.00860122014061	0.0105702431186	0.0967258250325	-0.0226575966759	0.103934187069	22.4437054971	2.19269258056	-30.3191206844

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 154 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 155 through 239 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -2 through 35 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 36 through 239 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid -2 through 35 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 36 through 118 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 119 through 157 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 158 through 239 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 4 through 18 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 19 through 56 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 57 through 78 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 79 through 118 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 119 through 157 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 158 through 239 )

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 842 molecules

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