PDB-8xdp: O-methyltransferase from Lycoris longituba complexed with Mg, SAH...

ID or keywords:

Entry

Database: PDB / ID: 8xdp

Title

O-methyltransferase from Lycoris longituba complexed with Mg, SAH, and 3,4-dihydroxybenzaldehyde

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: 1.75 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	8xdp.cif.gz	265.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8xdp.ent.gz	175.1 KB	Display	PDB format
PDBx/mmJSON format	8xdp.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/8xdp ftp://data.pdbj.org/pub/pdb/validation_reports/xd/8xdp	HTTPS FTP

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Related structure data

Related structure data	8xdoC 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

55.9 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)	49.781, 81.421, 118.454
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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 417 molecules

#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: Chemical	ChemComp-H6N / Protocatechuic aldehyde Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₆O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.19 Å³/Da / Density % sol: 43.76 %
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: 1.75→47.9 Å / Num. obs: 93813 / % possible obs: 100 % / Redundancy: 13.5 % / B_iso Wilson estimate: 21.53 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.108 / Net I/σ(I): 15.9
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 14.1 % / R_merge(I) obs: 1.366 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2710 / CC_1/2: 0.858 / % possible all: 100

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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: 1.75→47.9 Å / SU ML: 0.1693 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 19.354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1889	4726	5.04 %
R_work	0.1579	89087	-
obs	0.1594	93813	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: 28.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→47.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3881	0	16	411	4308

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0044	4175
X-RAY DIFFRACTION	f_angle_d	0.7605	5699
X-RAY DIFFRACTION	f_chiral_restr	0.0487	633
X-RAY DIFFRACTION	f_plane_restr	0.004	741
X-RAY DIFFRACTION	f_dihedral_angle_d	17.8883	1556

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 (%)
1.75-1.77	0.2965	180	0.2607	3047	X-RAY DIFFRACTION	99.91
1.77-1.79	0.3149	162	0.2577	2906	X-RAY DIFFRACTION	99.8
1.79-1.81	0.253	134	0.2389	2975	X-RAY DIFFRACTION	99.94
1.81-1.84	0.2637	125	0.2378	3018	X-RAY DIFFRACTION	99.9
1.84-1.86	0.3032	156	0.2243	2974	X-RAY DIFFRACTION	99.97
1.86-1.89	0.252	155	0.2214	2953	X-RAY DIFFRACTION	99.94
1.89-1.91	0.2851	167	0.2222	2984	X-RAY DIFFRACTION	99.94
1.91-1.94	0.2529	167	0.2033	2968	X-RAY DIFFRACTION	99.9
1.94-1.97	0.2487	171	0.1934	2932	X-RAY DIFFRACTION	100
1.97-2	0.2332	149	0.191	2956	X-RAY DIFFRACTION	99.9
2-2.04	0.2045	150	0.1751	2986	X-RAY DIFFRACTION	100
2.04-2.07	0.232	153	0.1659	3038	X-RAY DIFFRACTION	99.91
2.07-2.11	0.1792	150	0.1652	2899	X-RAY DIFFRACTION	99.97
2.11-2.16	0.2056	190	0.1624	2958	X-RAY DIFFRACTION	99.81
2.16-2.2	0.1874	165	0.1627	2957	X-RAY DIFFRACTION	99.97
2.2-2.26	0.2026	134	0.1625	2978	X-RAY DIFFRACTION	100
2.26-2.31	0.1776	166	0.1481	2914	X-RAY DIFFRACTION	99.9
2.31-2.38	0.1806	163	0.1523	3012	X-RAY DIFFRACTION	100
2.38-2.44	0.1839	155	0.1544	2951	X-RAY DIFFRACTION	99.97
2.44-2.52	0.1782	166	0.1582	2974	X-RAY DIFFRACTION	100
2.52-2.61	0.231	158	0.15	3009	X-RAY DIFFRACTION	100
2.61-2.72	0.1938	132	0.1539	2976	X-RAY DIFFRACTION	100
2.72-2.84	0.1803	166	0.1626	2944	X-RAY DIFFRACTION	100
2.84-2.99	0.1939	143	0.159	2987	X-RAY DIFFRACTION	100
2.99-3.18	0.185	150	0.1525	2974	X-RAY DIFFRACTION	100
3.18-3.43	0.1889	198	0.1405	2899	X-RAY DIFFRACTION	100
3.43-3.77	0.1468	141	0.1338	3026	X-RAY DIFFRACTION	100
3.77-4.31	0.1192	184	0.1203	2940	X-RAY DIFFRACTION	100
4.32-5.43	0.1704	139	0.1293	2986	X-RAY DIFFRACTION	99.94
5.44-47.9	0.1943	157	0.1655	2966	X-RAY DIFFRACTION	99.81

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	0.157449926905	-0.309739227862	-0.0289069127592	0.211318771084	0.0024432804464	0.0461490282243	0.0996136365654	-0.0151432987344	-0.0818633045053	-0.0795934747681	-0.0605413027751	-0.105347939278	0.00316652977207	-0.140693630973	0.000115333668733	0.279686293166	-0.00709890488284	0.0137793149286	0.232551432147	0.00113663878056	0.300643415401	-2.90384886034	-3.95289599342	14.5473648279
2	0.0389085277463	-0.0364461064833	-0.0281420369852	0.0552870241362	0.00422718869314	0.12256978634	0.0362208761587	-0.00548323729749	-0.115328609857	-0.0865040851024	0.0223821406064	0.22447101824	0.0100412921091	-0.174095915051	-4.84261134129E-5	0.170241155479	-0.00981142234483	-0.00438507796704	0.193186349841	0.00844810549094	0.201785019619	-5.05458970895	9.70077419411	32.2696585753
3	0.0126789739557	0.0347985327711	0.063577350506	0.0579351874307	-0.0722955936861	0.225519811698	-0.0521884117592	0.129636091718	-0.104381449576	0.0163356613012	-0.00728242863488	0.291256333936	0.0613787767835	-0.320256366751	2.76960570696E-5	0.200611960408	-0.00344891145106	-0.00297846609647	0.258705211763	-0.0139122274155	0.237409439231	-9.03267485822	11.1575444559	17.5824443479
4	0.10974263312	-0.100713334361	0.0448861944153	0.0677582323158	-0.0507298242924	0.107214791454	-0.0314513180282	0.0170254539072	-0.0334069694361	-0.0203152420168	0.0149098470678	-0.125079624179	-0.121454569264	-0.0105982798302	-9.52430405082E-7	0.22652336264	-0.00409807594258	0.00939828134186	0.206210437739	-0.0220769162292	0.193827917886	7.18259937367	20.3868708389	21.3624705732
5	0.135824191383	0.00629966614861	-0.0966702267462	0.103917173613	-0.0960008414523	0.305648824092	0.00558438944027	0.0118766121832	0.0853725733135	-0.131215414977	0.043999778036	-0.0320516004075	-0.186954407106	-0.085864648832	2.05413435472E-5	0.229506743492	0.00405917000786	-0.00777759207047	0.204218972637	-0.00181805651574	0.196538937553	-2.99153104974	20.7429097071	12.6115145877
6	0.174485301169	0.118757066678	0.0424977448744	0.215323383871	-0.13481960122	0.211217330747	0.0484482373606	0.258530150979	0.135127089839	-0.28516917223	0.00992060628938	0.101092101116	-0.294038078138	-0.0629777300179	-0.0170745620871	0.296714567692	-0.0170582320814	0.0376306082029	0.263925549898	0.0132942828495	0.189612415149	5.60029893873	21.7476631103	4.17994277471
7	0.149510364026	-0.0669704784442	0.0992498849208	0.0111251023771	-0.0254799712093	0.134783363371	-0.153281801444	0.223295429889	0.150014029402	-0.550055308667	0.0131089608141	-0.250534872571	-0.227402139525	0.104791533256	-0.00263279059794	0.34548830071	-0.072841201109	0.0625325978377	0.255512924172	0.0235856609755	0.241727247915	12.9487575468	21.2798214055	10.3454988888
8	0.193644328042	-0.0910998331158	0.110904918423	0.0494212573374	-0.0546056817802	0.142652074784	-0.0174519891782	0.110722905242	-0.0652673420556	-0.000966233943859	0.00942283394192	-0.158097911392	0.00311968722911	0.134428526202	-2.56839100921E-5	0.21440125095	-0.0314404499243	0.0475300253423	0.230471406194	-0.0157863995017	0.210687458486	14.1676748798	11.9730216451	11.2674845076
9	0.0935920457544	0.0180707577173	0.0565533825112	0.190872850675	-0.184004784176	0.0728409809819	0.0133740871426	0.137294543703	-0.432365793069	-0.222395049478	-0.00497300508704	-0.220050608099	0.143244645325	0.0523828485564	-0.0030766923049	0.273663462935	-0.0150892904148	0.0483551025272	0.225748071229	-0.0603214622413	0.297198674219	10.0057003007	-4.33524651196	13.6516396442
10	0.0742773311437	-0.126193127274	-0.0343133735215	0.1036189642	-0.0540771578878	0.111525626298	-0.0416785296126	-0.0260312836143	-0.136944411145	0.0476009309665	-0.0550662636395	-0.198257521853	0.0204525389141	0.115450392331	8.16887581076E-5	0.17231218377	-0.0268473719223	0.030621448217	0.198462770635	-0.023003901808	0.205101320836	17.7912807284	10.9678339822	19.3306964713
11	-0.0388251604197	0.10903409049	-0.0165378990061	0.0512241646293	-0.103300041153	0.0405701658508	0.00728965648174	-0.229025036946	-0.27124773973	0.08425251525	0.190475346178	0.153157333562	0.275508784189	0.346727393078	-0.000510131627483	0.397327654761	0.0676039806016	0.00950282162351	0.438602334252	0.0948385937305	0.415912568653	11.6929199636	-5.16089991916	45.7916846794
12	0.0301752249175	-0.0195688232797	0.0606748182588	0.18279605236	0.22122909059	0.225679085349	-0.0093662850178	0.0497159722189	-0.138905710995	0.0153100048976	0.00886858820681	-0.0824277841592	0.196040794576	0.15903004206	-4.57193238E-5	0.213374460863	0.0179288621212	-0.00608230496654	0.205126651519	-0.00120906321441	0.274575114189	22.5738115272	-0.00851258053878	34.3745342532
13	0.91872379784	-0.234674467917	0.0444747058639	0.329441455345	-0.0208097240491	0.727146003252	0.0126527767196	-0.0882277829496	0.0698976874491	0.0371016195402	0.0106507521474	-0.151982252941	-0.121669503156	0.129879187259	-3.4190775225E-6	0.194692615621	-0.02227740524	-0.0110297784902	0.198578329299	-0.0184771016493	0.216122141404	20.84673028	17.9690867252	42.408914841
14	0.285270449509	0.108801051817	0.282317507535	0.272201779814	0.163613856736	0.400259193301	-0.00010803569647	-0.0790221378993	-0.0413370164972	0.049977321953	0.0213467940722	-0.0033038133531	0.031287809247	-0.0572019632323	6.24984511673E-6	0.187810988238	0.00362939362413	0.0151521828888	0.179854775077	0.00609644875974	0.175444385426	3.8414618037	11.9933197584	41.1930000365

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 78 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 79 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 157 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 158 through 184 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 185 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 56 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 57 through 171 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 172 through 239 )

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