PDB-8xdo: O-methyltransferase from Lycoris longituba complexed with Mg and SAH

ID or keywords:

Entry

Database: PDB / ID: 8xdo

Title

O-methyltransferase from Lycoris longituba 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
Similarity search - Function

Biological species

Lycoris longituba (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.37 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	8xdo.cif.gz	275.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8xdo.ent.gz	180.8 KB	Display	PDB format
PDBx/mmJSON format	8xdo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xdo_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	8xdo_full_validation.pdf.gz	2 MB	Display
Data in XML	8xdo_validation.xml.gz	27.3 KB	Display
Data in CIF	8xdo_validation.cif.gz	42.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xd/8xdo ftp://data.pdbj.org/pub/pdb/validation_reports/xd/8xdo	HTTPS FTP

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Related structure data

Related structure data	8xdpC 8xdqC 8xdrC 8xdsC 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)	49.637, 81.183, 118.027
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: 27443.348 Da / Num. of mol.: 2 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.: 685 / 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: 43.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 21 % (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: 1.37→47.73 Å / Num. obs: 193630 / % possible obs: 100 % / Redundancy: 13.5 % / B_iso Wilson estimate: 12.65 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.089 / Net I/σ(I): 16.9
Reflection shell	Resolution: 1.37→1.39 Å / Redundancy: 13 % / R_merge(I) obs: 1.249 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4947 / CC_1/2: 0.797 / % 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: 1.37→47.73 Å / SU ML: 0.1167 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 16.3887
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1683	9712	5.02 %
R_work	0.1449	183918	-
obs	0.1461	193630	99.94 %

Solvent computation

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

Displacement parameters

B_iso mean: 18.72 Å²

Refinement step

Cycle: LAST / Resolution: 1.37→47.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3886	0	6	685	4577

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0122	4287
X-RAY DIFFRACTION	f_angle_d	1.3196	5865
X-RAY DIFFRACTION	f_chiral_restr	0.099	648
X-RAY DIFFRACTION	f_plane_restr	0.0081	769
X-RAY DIFFRACTION	f_dihedral_angle_d	17.983	1621

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 (%)
1.37-1.39	0.2835	299	0.2615	6142	X-RAY DIFFRACTION	99.61
1.39-1.4	0.2348	293	0.2324	6141	X-RAY DIFFRACTION	99.67
1.4-1.42	0.226	299	0.2201	6234	X-RAY DIFFRACTION	99.86
1.42-1.44	0.2315	336	0.2087	6034	X-RAY DIFFRACTION	99.8
1.44-1.46	0.2156	327	0.2048	6159	X-RAY DIFFRACTION	99.86
1.46-1.48	0.2253	333	0.1885	6126	X-RAY DIFFRACTION	99.95
1.48-1.5	0.2257	320	0.1816	6084	X-RAY DIFFRACTION	99.95
1.5-1.52	0.2035	378	0.1753	6062	X-RAY DIFFRACTION	99.97
1.52-1.54	0.1718	375	0.1701	6194	X-RAY DIFFRACTION	99.97
1.54-1.57	0.1858	300	0.1655	6044	X-RAY DIFFRACTION	99.95
1.57-1.6	0.1883	357	0.1571	6127	X-RAY DIFFRACTION	99.95
1.6-1.62	0.1827	332	0.1571	6130	X-RAY DIFFRACTION	100
1.62-1.66	0.1766	297	0.1458	6174	X-RAY DIFFRACTION	99.97
1.66-1.69	0.1788	319	0.15	6126	X-RAY DIFFRACTION	99.98
1.69-1.73	0.1735	306	0.1486	6151	X-RAY DIFFRACTION	99.97
1.73-1.77	0.1761	331	0.1446	6164	X-RAY DIFFRACTION	100
1.77-1.81	0.1643	298	0.1423	6086	X-RAY DIFFRACTION	99.95
1.81-1.86	0.1461	323	0.1378	6148	X-RAY DIFFRACTION	100
1.86-1.91	0.1814	285	0.1407	6205	X-RAY DIFFRACTION	99.94
1.91-1.98	0.1538	321	0.1367	6131	X-RAY DIFFRACTION	100
1.98-2.05	0.1386	321	0.1318	6112	X-RAY DIFFRACTION	100
2.05-2.13	0.1542	356	0.1325	6080	X-RAY DIFFRACTION	100
2.13-2.23	0.148	299	0.1361	6155	X-RAY DIFFRACTION	100
2.23-2.34	0.1585	317	0.1316	6122	X-RAY DIFFRACTION	99.98
2.34-2.49	0.1618	365	0.1377	6150	X-RAY DIFFRACTION	100
2.49-2.68	0.164	314	0.1375	6120	X-RAY DIFFRACTION	100
2.68-2.95	0.182	336	0.1479	6128	X-RAY DIFFRACTION	100
2.95-3.38	0.163	314	0.1375	6137	X-RAY DIFFRACTION	99.98
3.38-4.26	0.1364	298	0.1211	6153	X-RAY DIFFRACTION	99.98
4.26-47.73	0.1698	363	0.1393	6099	X-RAY DIFFRACTION	99.92

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	0.165638883842	-0.14269647126	-0.111930353127	0.18348296399	0.0235545591249	0.0750287776435	0.0525292858788	0.0373938981996	-0.0158622554953	-0.0485337745457	-0.0256532168179	-0.0123366534191	0.0514456831153	0.0546355715481	-1.2227517648E-5	0.179716283564	-0.00631488258172	-0.000815726994236	0.14718767708	-0.00741800577994	0.154971271824	-2.88943763233	-3.81017749641	14.5525669973
2	0.152172151786	0.0123105591992	-0.0123132205018	0.0367190009444	-0.0133457971196	0.0173749132623	0.0227095923489	0.00201699819531	-0.0946669426081	-0.0364026165649	0.00414370735923	0.0844195553934	-0.0141041382191	-0.0276095284669	-6.16691105934E-5	0.10623943383	-0.000771451599497	-0.000647640546992	0.111590804163	-0.00242932677962	0.127214384936	-5.04599478177	9.92571505597	32.1448513517
3	0.0567252984243	0.102988227507	0.0529468591574	0.118948350307	0.00328735885231	0.177191780009	-0.0490412725451	0.0366341515207	-0.0784743620042	0.066491194771	-0.00289687379243	0.125002685694	0.0668930010553	-0.142337597647	-0.000751886775411	0.113295617907	-0.00954274122798	0.00283940026474	0.148182408343	-0.0178553498629	0.138426906555	-8.9231322298	10.9583301469	17.3367483342
4	0.0854887432617	-0.089745826057	-0.0506122626443	0.136988037057	-0.0542804671633	0.204507723575	-0.00176536251805	-0.0224763252373	0.00498474815232	0.00560146299091	0.0100598656868	-0.0187902104034	-0.072742080494	0.00810232042674	2.06859400912E-6	0.108120917804	-0.00750589551473	0.00853610947131	0.100531113131	-0.0084587642946	0.0939337326903	4.61541286025	20.0043453307	19.3881436398
5	0.0799677740642	-0.0117170868762	-0.00816658705509	0.0601149263929	-0.133705449919	0.197898232704	0.0145395947003	0.0620174590817	0.100365764957	-0.140506421268	0.030372927416	0.0250933595759	-0.156225925455	-0.103283475443	4.1440163414E-5	0.161843518986	0.0134436411462	-0.00172291244562	0.158229758765	-0.00117109131545	0.135778586902	-3.64238000631	21.7311694675	10.3079010946
6	0.252473515975	0.156358880667	0.205217272795	0.459831870383	0.00496095485345	0.386862106179	0.0225514946833	0.202137528522	0.0887378433384	-0.232137769655	-0.0167975904314	0.0348767543458	-0.189087117372	0.0117738056915	-0.136088451697	0.17409450757	-0.00675062022144	0.0223188831178	0.162588523908	0.0113528752115	0.110018320499	5.5869693952	21.7207998589	4.06847915092
7	0.309717285891	-0.0617855225017	0.177167305218	0.17006344039	0.146679574841	0.366271452322	-0.0402718327186	0.179491431067	0.0661932650863	-0.16584430702	0.0332851349697	-0.0201149019148	-0.0776661294436	0.079466080067	-0.00479469334089	0.152393782227	-0.0277696326801	0.0272918519687	0.151402121504	0.00365418417428	0.122216180495	13.8019095853	16.5514182258	8.61830801405
8	0.35287897737	-0.147770747185	0.152705688285	0.0689399311199	-0.0540944889515	0.215246655911	0.00240211963903	0.080272737071	-0.0850709646482	-0.0478466846647	0.0380845911275	-0.0386205677208	0.0239337194391	0.0448838707833	0.000494812287251	0.117816864478	-0.00561098409014	0.010792596055	0.108245515114	-0.0143684342351	0.125910211113	9.76969312094	1.83978376361	16.2332671967
9	0.0599682449809	0.0537215685052	-0.0349454154081	0.039153917862	0.000701827362556	0.045949059625	-0.0276164780996	0.137669366233	-0.122932467258	-0.09418970708	0.0319111171121	-0.0898474067766	0.0616804686087	0.0695243003314	-0.000885355135125	0.151744595176	-0.0075254738156	0.0360940090939	0.135446089637	-0.0244836738595	0.142873132098	12.7649948378	-1.52900572832	11.8551359428
10	0.119106837063	-0.134364431156	0.0408452377554	0.0981585405591	-0.0703668296825	0.11951304984	-0.0110149227545	0.0811463215487	-0.0521661661189	-0.0138164907209	-0.0133438459194	-0.080171008728	0.0288460372257	0.040361348651	0.000386089497294	0.106819351589	-0.0112553290334	0.0166947986232	0.122965733505	-0.00344580302207	0.12318914345	18.0405575864	11.1946216803	19.3434625067
11	0.00573017793385	0.028386568824	-0.05195796966	0.10459308286	-0.020244489875	0.0675376767256	-0.01431952261	-0.132379937922	-0.0549699336564	0.0808127568856	0.0749108615651	-0.00816940000548	0.19008648443	0.10506825338	-9.97725870428E-5	0.190478392592	0.0131285014842	-0.0106948945244	0.199268357496	0.0242084699656	0.19736069032	11.4287429393	-4.98230993876	45.4140712004
12	0.0597093987554	0.0171895949329	0.0340890643023	0.0395416609101	-0.00766987797479	0.0973213160396	-0.0046568898666	-0.0681202846147	-0.0922741866508	-0.00955599697743	0.0202146677341	-0.0295259224204	0.0631518057243	0.037022588554	1.80755432006E-5	0.129145992847	0.00125674020561	0.00254601383115	0.130472975672	0.00200244897924	0.145178454342	19.5744643202	-0.736043050852	26.307590075
13	0.322476812552	0.0791254354442	-0.0488051201287	0.252481052295	0.227160331874	0.595244986041	-0.00360422908843	-0.00290427855216	-0.0166254941199	0.0106002121682	0.00272826119745	-0.0267846950145	0.0295561434217	0.039241076963	-9.27459959052E-6	0.102408741004	0.00058497336173	0.0057322719967	0.106270471963	0.00182655845441	0.108456765436	22.1955852877	9.7387729794	36.867688878
14	0.33651653167	-0.208638205179	0.138773530643	0.245438730228	0.0532359522671	0.476220405218	-0.0157326381089	-0.0961881147755	0.120187817245	0.0387432201941	0.00686884260707	-0.106894981298	-0.0975212952499	0.0891587564541	-0.000405677610224	0.118453055182	-0.016212062394	-0.00603049720065	0.129261084283	-0.00903313211172	0.137368531076	23.7149723129	19.0922324032	44.9030558072
15	0.449048773035	0.0557285741619	0.148170202703	0.330083870267	-0.00786185760708	0.246369867368	0.0087204755262	-0.058556411687	-0.0117826668437	0.0357611814219	-0.00728498622476	-0.00470541814051	-0.00145845601052	-0.0355530271316	-3.01715255802E-6	0.115122823911	0.00146748503792	0.00611263682523	0.102542800923	-0.00177646865172	0.0999441939469	4.44377692417	13.3872183762	42.2820742136

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 35 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 56 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 57 through 92 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 93 through 118 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 119 through 142 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 143 through 171 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 172 through 198 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 199 through 217 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 218 through 239 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -2 through 18 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 19 through 35 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 36 through 92 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 93 through 157 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 158 through 239 )

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