PDB-8xds: O-methyltransferase from Lycoris longituba F186Y variant complexe...

ID or keywords:

Entry

Database: PDB / ID: 8xds

Title

O-methyltransferase from Lycoris longituba F186Y variant complexed with Mg and SAH

Components

norbelladine O-methyltransferase

Keywords

TRANSFERASE / O-methyltransferase family protein / LlOMT

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

Lycoris longituba (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.97 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	8xds.cif.gz	263.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8xds.ent.gz	173.9 KB	Display	PDB format
PDBx/mmJSON format	8xds.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/xd/8xds ftp://data.pdbj.org/pub/pdb/validation_reports/xd/8xds	HTTPS FTP

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Related structure data

Related structure data	8xdoC 8xdpC 8xdqC 8xdrC 8xdtC 8xduC 8xdvC 8xdyC 8xe0C 8xe2C 8xe3C 8xe4C 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 O-methyltransferase

B: norbelladine O-methyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	49.490, 81.229, 118.468
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

#1: Protein	norbelladine O-methyltransferase Mass: 27459.348 Da / Num. of mol.: 2 / Mutation: F186Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lycoris longituba (plant) / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A0A6B9TNK2
#2: 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
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H₂O
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: 2.17 Å³/Da / Density % sol: 43.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 24% (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: 1.045 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 19, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.045 Å / Relative weight: 1
Reflection	Resolution: 1.97→47.86 Å / Num. obs: 65158 / % possible obs: 99.9 % / Redundancy: 11.8 % / B_iso Wilson estimate: 21.36 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.184 / Net I/σ(I): 11.5
Reflection shell	Resolution: 1.97→2.02 Å / Redundancy: 12.1 % / R_merge(I) obs: 1.192 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2376 / CC_1/2: 0.77 / % possible all: 99.8

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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: 1.97→47.86 Å / SU ML: 0.1952 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 18.5081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2015	3317	5.09 %
R_work	0.1598	61841	-
obs	0.1618	65158	99.91 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.36 Å²

Refinement step

Cycle: LAST / Resolution: 1.97→47.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3884	0	6	449	4339

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	4133
X-RAY DIFFRACTION	f_angle_d	0.7104	5642
X-RAY DIFFRACTION	f_chiral_restr	0.0464	630
X-RAY DIFFRACTION	f_plane_restr	0.0038	734
X-RAY DIFFRACTION	f_dihedral_angle_d	18.4275	1543

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 (%)
1.97-2	0.2718	138	0.2437	2544	X-RAY DIFFRACTION	99.55
2-2.03	0.2734	149	0.2417	2569	X-RAY DIFFRACTION	99.67
2.03-2.06	0.293	122	0.2103	2593	X-RAY DIFFRACTION	99.74
2.06-2.09	0.2378	166	0.2072	2507	X-RAY DIFFRACTION	99.78
2.09-2.13	0.2143	132	0.1996	2600	X-RAY DIFFRACTION	99.96
2.13-2.17	0.2191	142	0.1947	2603	X-RAY DIFFRACTION	99.82
2.17-2.21	0.2361	122	0.1926	2583	X-RAY DIFFRACTION	99.85
2.21-2.26	0.2565	176	0.1868	2541	X-RAY DIFFRACTION	99.93
2.26-2.3	0.2271	140	0.1776	2545	X-RAY DIFFRACTION	99.93
2.3-2.36	0.2343	127	0.1753	2607	X-RAY DIFFRACTION	99.96
2.36-2.42	0.183	159	0.168	2551	X-RAY DIFFRACTION	99.96
2.42-2.48	0.2396	145	0.1628	2572	X-RAY DIFFRACTION	100
2.48-2.56	0.2028	117	0.1638	2613	X-RAY DIFFRACTION	100
2.56-2.64	0.2034	146	0.16	2570	X-RAY DIFFRACTION	100
2.64-2.73	0.2077	133	0.162	2586	X-RAY DIFFRACTION	100
2.73-2.84	0.2203	126	0.1633	2571	X-RAY DIFFRACTION	100
2.84-2.97	0.2307	122	0.1695	2623	X-RAY DIFFRACTION	100
2.97-3.13	0.2108	147	0.1598	2569	X-RAY DIFFRACTION	100
3.13-3.32	0.1603	136	0.1421	2572	X-RAY DIFFRACTION	100
3.32-3.58	0.1916	158	0.1407	2561	X-RAY DIFFRACTION	100
3.58-3.94	0.1323	111	0.1252	2607	X-RAY DIFFRACTION	100
3.94-4.51	0.1359	124	0.1136	2596	X-RAY DIFFRACTION	100
4.51-5.67	0.1918	139	0.1431	2566	X-RAY DIFFRACTION	100
5.68-47.86	0.2022	140	0.1645	2592	X-RAY DIFFRACTION	99.74

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	0.492415962728	-0.269325867504	-0.480668680821	0.706851937878	0.811767010776	1.65597821256	0.0131039036126	0.0290984669336	-0.120400837732	-0.140906376445	-0.033800808449	-0.0446262459694	0.0537658386787	-0.0412840085269	0.0263901622231	0.217924656086	-0.0022384965958	-0.00932535663596	0.205716549788	-0.00496795638017	0.266255410754	-3.52973584868	-0.444894537205	21.9190508715
2	0.786135633463	-0.129828524694	-0.155083988721	0.847856040753	0.194310579152	1.73221642132	-0.00558407592884	0.0533745652919	0.0336951032041	-0.0525671247217	0.0219688334824	0.0531417132989	-0.126634557257	-0.088954453372	-0.0169439344523	0.167207868027	0.014092580787	-0.00278252163911	0.150505949656	0.00324255287379	0.155477062296	-0.878610777933	17.4797285342	18.6180364526
3	1.6028487287	-0.283475640535	-0.291805376261	1.21546542912	0.320071331158	1.66573989731	0.0564162211904	0.328860134593	0.170522433958	-0.317976114024	0.029760349848	0.0401302765296	-0.219619966659	-0.123595393638	-0.0928638862522	0.273850725978	4.09761938243E-5	0.00133144096418	0.210308443562	0.0409906601877	0.17768261366	0.563346889605	20.9049378782	6.22467440844
4	1.55997493595	-0.28480301614	0.334946169706	1.22887527877	0.542971328709	1.68128056136	-0.0239272521271	0.315390808091	0.179986593857	-0.255674716087	0.0685711248357	-0.0791960247871	-0.136482360411	0.24267512584	-0.0393261952184	0.24311140115	-0.0391943681017	0.0318856418805	0.239761618168	0.0160475869224	0.203625488211	13.751357777	16.0939698913	8.86795938083
5	1.38785827426	0.467992294071	0.284226641613	1.02729688819	-0.234099625183	0.721688085485	0.00191328118333	0.159737853599	-0.243420299314	-0.18750131724	0.0419796406102	-0.115468791984	0.103803304537	0.0516517479884	-0.0226876195856	0.202478436097	0.00193881907842	0.0234302038622	0.190018634348	-0.0333905188431	0.187737799465	10.8261427212	0.120094760353	14.4613151176
6	1.01001408877	-0.191318307306	-0.796121891485	0.494352363657	-0.208459090768	1.00939976693	-0.0921098140132	0.100897201051	-0.0524785455763	-0.0702645347042	0.0365715769208	-0.116078854186	0.0351441279567	0.134380508061	0.0651167792493	0.180657872867	-0.0197719746813	0.02123496835	0.221860519559	-0.0206858459695	0.177685172731	18.0283536653	10.9112381659	19.4647392527
7	0.381493357976	0.146199957176	-0.802928106662	0.723144299447	-0.168496062678	1.70017054775	-0.046486408312	-0.073738198601	-0.146697952691	0.164274199364	0.12001429515	-0.0731327759138	0.20332200883	0.533580101675	-0.170210540886	0.273192599276	0.0354274248052	0.0131502639264	0.276396970126	0.0350715944283	0.279980849605	11.8735031132	-5.22035665124	46.3064897576
8	2.73510789137	0.588415822807	0.745160955782	1.35544662561	0.573896432644	1.37736383888	0.0959183366917	-0.159913135385	-0.408326780406	-0.0239787038933	-0.0484336018824	-0.162775980119	0.169459170269	0.0875339894849	-0.0182475986144	0.170420148905	0.0239668113187	-0.0114424061502	0.16858340485	-0.00201366013896	0.195445721898	19.4111546746	-1.1003436923	26.3890844132
9	0.882598020125	-0.168900227131	0.0732989027014	1.09103797223	-0.0771098465025	1.71845217812	-0.0103159718104	0.00672950275077	-0.0301598682675	0.0316429250298	0.0429997448821	-0.0411667521989	0.0417511960209	0.0563792963334	-0.0347376602789	0.140012085564	-0.00256264099043	0.0109142427523	0.172555351473	-0.0202473033744	0.166822015505	22.3034320585	9.40607812942	36.9663201357
10	1.41064908849	-0.255500305992	0.228031380606	0.778499429298	0.246028689751	1.58385389507	-0.00955690602297	-0.154197930001	0.147822525289	0.0863746743076	0.0259500809928	-0.148187323142	-0.174995365187	0.127213545954	-0.0227903381983	0.185341744789	-0.0250193713979	-0.00945388523791	0.189494480575	-0.0269687480427	0.21801600966	23.8337395159	18.6701244088	44.9396876371
11	0.774105876374	0.223864770215	-0.0816925593045	0.829863312566	-0.147788930258	0.903760540672	-0.00911781835063	-0.143970733112	0.00508820867518	0.0895373031878	-0.0863277526693	0.0187076242288	-0.099023755604	0.0170099884675	0.0892618027281	0.165108509567	0.0042216954379	0.00453430357502	0.157009594577	-0.00857443947677	0.156754103582	9.29820660082	19.0041185882	43.3750798487
12	0.523328345245	0.119231907116	-0.0851385379611	2.11924875549	-0.649802444829	1.31597201532	0.0102359066963	-0.107883959783	-0.0365633730715	0.175123034797	0.134563771021	0.0430552199317	0.0680661044132	-0.0698930114566	-0.107648701904	0.174170542578	-0.00416262808474	0.00395597233303	0.188492877051	0.0111267463876	0.1622970192	1.05480255965	4.88161513171	46.0454544178
13	0.621435586258	-0.327819201309	-0.0772174378683	1.13067931581	0.571741752463	0.454047125522	-0.0536063627095	-0.0782423482559	0.0183057607331	-0.0300596352612	0.0318349467189	-0.105601669954	-0.0345034057087	-0.0169695082139	0.00355329947983	0.195120607693	0.00201987137773	0.0133218347341	0.164204014838	-0.0125729544818	0.167492325545	4.76588636197	18.9765758564	35.5147948024

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 105 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 142 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 143 through 171 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 172 through 217 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 218 through 239 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -2 through 18 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 19 through 35 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 36 through 92 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 93 through 157 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 158 through 184 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 185 through 216 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 217 through 239 )

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