PDB-8z8o: norbelladine 4'-O-methyltransferase Y186F complexed with Mg and SAH

ID or keywords:

Entry

Database: PDB / ID: 8z8o

Title

norbelladine 4'-O-methyltransferase Y186F complexed with Mg and SAH

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: 1.71 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	Apr 22, 2024	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	8z8o.cif.gz	502.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8z8o.ent.gz	341.3 KB	Display	PDB format
PDBx/mmJSON format	8z8o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8z8o_validation.pdf.gz	4 MB	Display	wwPDB validaton report
Full document	8z8o_full_validation.pdf.gz	4 MB	Display
Data in XML	8z8o_validation.xml.gz	46.2 KB	Display
Data in CIF	8z8o_validation.cif.gz	68.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/8z8o ftp://data.pdbj.org/pub/pdb/validation_reports/z8/8z8o	HTTPS FTP

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Related structure data

Related structure data	8xdoC 8xdpC 8xdqC 8xdrC 8xdsC 8xdtC 8xduC 8xdvC 8xdyC 8xe0C 8xe2C 8xe3C 8xe4C 8xe5C 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

D: Norbelladine 4'-O-methyltransferase

hetero molecules

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

2

B: Norbelladine 4'-O-methyltransferase

C: Norbelladine 4'-O-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.416, 79.806, 91.621
Angle α, β, γ (deg.)	90.000, 93.954, 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

#1: Protein	Norbelladine 4'-O-methyltransferase / NpN4OMT Mass: 27381.084 Da / Num. of mol.: 4 / Mutation: Y186F 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, norbelladine O-methyltransferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 949 / 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: 2.15 Å³/Da / Density % sol: 42.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 7.0)

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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: 1.035 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.035 Å / Relative weight: 1
Reflection	Resolution: 1.71→45.7 Å / Num. obs: 99875 / % possible obs: 99.9 % / Redundancy: 4.3 % / B_iso Wilson estimate: 16.54 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.074 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.71→1.74 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.523 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4980 / CC_1/2: 0.769 / % 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: 1.71→45.7 Å / SU ML: 0.177 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1863	2002	2.01 %
R_work	0.1568	97842	-
obs	0.1574	99844	99.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 21.47 Å²

Refinement step

Cycle: LAST / Resolution: 1.71→45.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7730	0	24	949	8703

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	8183
X-RAY DIFFRACTION	f_angle_d	0.889	11164
X-RAY DIFFRACTION	f_chiral_restr	0.056	1239
X-RAY DIFFRACTION	f_plane_restr	0.0049	1444
X-RAY DIFFRACTION	f_dihedral_angle_d	20.996	3039

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 (%)
1.71-1.75	0.2375	128	0.2207	6966	X-RAY DIFFRACTION	99.99
1.75-1.8	0.2553	162	0.2078	6956	X-RAY DIFFRACTION	99.97
1.8-1.85	0.2334	137	0.198	6957	X-RAY DIFFRACTION	99.99
1.85-1.91	0.2454	145	0.1832	6963	X-RAY DIFFRACTION	99.99
1.91-1.98	0.196	141	0.164	6968	X-RAY DIFFRACTION	99.97
1.98-2.06	0.2028	147	0.162	6976	X-RAY DIFFRACTION	100
2.06-2.15	0.1895	132	0.1611	7003	X-RAY DIFFRACTION	99.92
2.15-2.27	0.1597	147	0.1532	6980	X-RAY DIFFRACTION	99.93
2.27-2.41	0.2013	148	0.156	6972	X-RAY DIFFRACTION	99.92
2.41-2.6	0.1936	145	0.163	6958	X-RAY DIFFRACTION	99.72
2.6-2.86	0.2009	136	0.1608	6999	X-RAY DIFFRACTION	99.6
2.86-3.27	0.1857	144	0.1556	6993	X-RAY DIFFRACTION	99.8
3.27-4.12	0.1451	144	0.1306	7020	X-RAY DIFFRACTION	99.69
4.12-45.7	0.1639	146	0.142	7131	X-RAY DIFFRACTION	99.63

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	0.215816227354	0.0268960147364	0.0422633485581	0.0691636500225	0.000930655263173	0.000676252513115	-0.0195601258956	-0.0992279648002	0.110453418107	0.0868781697178	-0.0142919316443	-0.0868947865585	-0.0126553316522	0.0333624401769	-9.67344902471E-5	0.119852421561	0.00319897918986	-0.0154913860342	0.113943810533	-0.00811718733132	0.166844998229	-0.143831655495	-4.7610692108	49.0571141082
2	0.799194843354	-0.025462052717	-0.424740423034	0.0614699316932	-0.0288685825681	0.205021185756	-0.0166726577495	-0.101465469187	0.0142742933115	0.024836457201	0.0477977510498	-0.0228671864992	-0.0379232541179	0.051139263396	0.0345355555473	0.090188758565	0.00207507500892	-0.00897142573446	0.0831903707528	-0.00851956018061	0.0897035214717	7.37633531659	-16.6191782061	45.4016787105
3	1.08915145908	-0.279621256268	-0.0037995918036	0.131491783252	0.15044598172	0.281073777449	-0.0539535000446	0.120290594537	-0.0356525067255	0.0298875346929	0.0202101235863	-0.104703060733	0.0502404023432	0.138206320572	-0.00185175331761	0.0961912191514	-0.00497737194241	0.000397788266116	0.131103902097	-0.00204215517503	0.115852397579	17.3008610484	-19.4845855056	36.9069193864
4	0.769838178354	-0.349417086457	-0.263374241112	0.219085500029	0.0636298161292	0.205146743998	0.0278086973276	0.10677810593	0.165449407905	-0.00218830661511	0.0181794667108	-0.11324854798	-0.00134448704612	0.0326564716142	0.0190867603133	0.101877960784	-0.0156010163115	0.00259606287239	0.103972032017	0.0120851192774	0.114367637039	8.24524813712	-4.44627982585	30.5344427609
5	0.0991137077563	0.131858393174	0.120258905353	0.273934086717	0.0218050527246	0.0960965760569	-0.039120498936	0.0214667937356	0.0527426004949	-0.053135075527	0.00435312352461	-0.108768072459	-0.0673344647563	0.0389195740545	-5.34058399561E-5	0.144251101041	-0.00754762278373	0.0252065443821	0.104942248237	0.0100696840891	0.141726522511	32.778758397	-7.46237305272	89.6119939768
6	0.270225308255	0.0215916875711	-0.363276991698	0.310181719938	0.0123814744702	0.458434514718	-0.0172266036706	-0.0310332122435	0.0233332017053	0.00372366241528	0.0605552088226	-0.028311999001	-0.0641106979822	0.0349299559702	0.061765963562	0.115362634276	-0.00845325065325	0.00894838831128	0.0750751240074	-0.0148520094241	0.094302249271	33.595345584	-19.9572289827	84.1735232496
7	0.795493820199	-0.116139032915	-0.244064174215	0.386391143989	0.153459197854	0.439360370712	-0.0130981436596	0.217938332575	-0.0585101444778	-0.0563569156315	0.0503811736614	-0.100025227465	0.0755120363708	0.0273659080235	0.110961700735	0.137875832309	-0.0275808226599	0.0197269766512	0.135051326315	-0.0215115538482	0.112615357836	35.8266537573	-23.1527617037	71.6633698576
8	0.341336742133	-0.0507076847276	-0.11731386114	0.189759855487	0.0850376687913	0.358699495149	-0.00103415583069	0.126837358162	0.0523043441102	-0.0746476580854	0.0265411638399	-0.0279980640068	-0.053369323387	-0.0250195789071	0.0325684647493	0.13755633863	-0.0241222329769	-0.00779265971919	0.117255495557	0.0131245633696	0.0913222184605	25.0206482959	-7.99735080801	72.5483012065
9	0.0151962670805	0.0293823169016	0.0245338102845	0.041627334451	0.0946996315488	0.0789840913646	-0.0178379915693	-0.0466351717165	0.105418779712	0.0849137644891	0.00420153798356	0.0372498341828	0.0760866183676	-0.205446961955	-0.000333634769022	0.208055812262	-0.0311831063473	0.00936966669188	0.177503148176	0.0253723719074	0.213836196123	8.05946375505	-0.379554524654	95.5326796991
10	0.10853286509	0.0891043103277	-0.110511105577	0.0400938076447	-0.0706192357782	0.0488393736256	-0.00327411039364	0.156903270225	0.0690901009136	-0.00846749169949	0.0489144953854	0.00938604724323	-0.125718843044	-0.062319911926	0.0204302056503	0.147028271828	0.012351610735	-0.0152370569054	0.155892667556	0.048875191803	0.132620223659	8.56731366368	-3.48805827317	76.6162948121
11	0.169532466338	0.116671072382	-0.0519160491228	0.0729789687505	-0.072192331688	0.204467383767	0.000370612943647	0.0883502354798	0.00858166373324	0.0467507832129	0.0194412673914	0.0134991005574	-0.0213978843114	-0.0511312082946	0.00941594975426	0.114736517452	-0.00636188670705	0.00641593720895	0.116322044586	0.00857761783523	0.104467105335	6.61519554101	-14.1843262556	83.606055938
12	0.492578309042	-0.102674395937	-0.0412957673115	-0.0335529963369	-0.150339255605	0.401352004592	-0.0106524910917	0.0457073319336	-0.0989598359779	-0.0105414773084	0.0317974135814	0.127756511543	0.0616024709666	-0.250999106845	-2.64272398221E-5	0.107711849299	-0.0310080243626	-0.00296365597342	0.166723871739	0.0105135708295	0.125287700681	-1.91377822857	-21.2407746215	85.6131505971
13	0.157299197641	0.00823663868074	0.0876577349255	0.0553888880598	-0.0803144849267	0.11096522529	-0.0151971450807	-0.0655825846503	-0.0257765097003	0.071262775493	0.0333062835641	0.0214056573568	0.0341280625119	-0.0816383291282	-2.53350542729E-7	0.1357747099	-0.00662314395264	0.0123117752838	0.103490165861	0.00544271975952	0.108318831544	8.70050328604	-21.7861929245	95.4496155099
14	0.0140650349285	-0.0120951683532	-0.0105201452064	0.0378647865116	0.100829904427	0.0949467192474	0.0172195137631	-0.0232757825252	0.0312690492633	0.0434923013642	0.0249612029817	0.00410996892139	-0.0029590706338	-0.022582958975	0.0315971924704	0.125316962606	-0.00067026680511	0.0145565858711	0.0758855012501	0.00567449103192	0.108819466008	14.2644366605	-8.71852107665	103.300326957
15	0.0394674613281	0.0375243502847	0.0506678925136	0.0380504260742	-0.0432395715312	0.08434860964	-0.0522571286762	-0.0118001313901	-0.0234442835767	-0.0368545333473	0.0658769637041	-0.0539304131525	0.0439881763473	-0.00961397306864	-0.00275420316836	0.140532750519	0.00514243967252	0.0130589555723	0.0613650414986	0.0103399752479	0.106775067231	17.7596177887	-22.501983872	92.490086511
16	0.0309484838065	0.0905114789292	0.0506897473333	0.187299895309	0.0320032844457	0.242396754437	0.0887299488401	-0.189100174122	0.167565256335	-0.0225105923675	-0.0167230388293	-0.153046312051	-0.0532452389533	0.257343828504	-0.000106672763796	0.154473882597	0.00539572414771	-0.00160838325526	0.181541087788	-0.0288378437674	0.230241553766	6.85417523941	-36.9057581291	56.7202215637
17	0.132848465519	-0.193376361681	-0.00328854572203	0.206534445108	-0.013191568107	0.0216506968647	-0.0568938775732	-0.293431276152	0.297928830803	0.0272302691497	0.0722239567049	-0.109379805623	-0.00440794525312	0.0154925951777	0.00197589405222	0.126490591425	0.00117741106145	-0.0220262032638	0.223962284053	-0.0888306985962	0.194091232302	7.24230554079	-41.5323153151	69.1275804322
18	0.0920961308801	0.0148125717705	-0.00265412957083	0.0651319413476	0.0626800118683	0.0441037225275	-0.0643457765458	-0.231965930941	-0.0572830301065	-0.0303866894446	0.103458656596	-0.0184568784155	-0.0100090281951	-0.0389592700161	-0.000153756053877	0.0858549558576	0.00600676922223	-0.00244354041717	0.153355011973	0.0213367361242	0.099742739691	2.17918421074	-57.3198473616	64.042746515
19	0.0267556153209	0.00604264587722	-0.0319021728823	0.133590972082	0.110020919951	0.104616984367	-0.149892899943	-0.355992826763	0.0675207399776	0.0944433097283	0.127437075664	-0.100789311166	0.0123464570433	0.150289708281	-0.00922935702815	0.101941130318	0.0233490898049	-0.0130275968704	0.22675202929	0.00758452063911	0.1086272554	11.2176532037	-55.1181202631	68.8526670035
20	-0.0033871425298	0.0128459552121	-0.0173700047187	0.320552470802	-0.0520462812198	0.641136967822	-0.205238489738	-0.3828706353	0.146776074817	0.175406835927	0.183327453471	-0.19725366053	0.146406858616	0.0722893361042	-0.0961645279366	0.161447555533	0.0480688062968	-0.0748128565092	0.443178808546	-0.0821341762763	0.122662074566	15.8161345551	-48.6486830771	75.0160139086
21	0.19124983834	0.343885797658	0.174055681585	0.866040963878	0.263336380707	0.45550293029	-0.0570389500057	-0.362554726337	-0.368525028749	0.0345855301069	0.111442925815	-0.322427001424	-0.0394979272128	0.0542499039678	0.048915107333	0.0902842783662	0.0568743144693	-0.0590832541661	0.289147176911	0.0573353618513	0.154961172346	19.0833432761	-62.0744948888	65.5282135737
22	0.342438475114	-0.00335942763474	0.220072607326	0.12241612556	0.0963758055179	0.21230365279	0.00459950987181	-0.0354924042441	-0.0650962000108	0.0194880799822	0.0599290181359	-0.0447200391833	0.0335338088333	0.127017887642	0.0448185125061	0.0893079033422	0.0148078861456	0.00323176387166	0.130113338332	0.00063653215799	0.143725449189	11.6431606835	-61.0274754599	55.7855313288
23	0.107307258015	0.0226247176751	-0.055625381845	0.0361882996009	0.00662544596597	0.18829495077	0.00695813591163	0.124075390459	0.220596937592	-0.0196323473344	-0.0836375864618	-0.178379959611	0.0695701209202	-0.127744402087	-0.00612701349193	0.122786158216	-0.029120369365	-0.000959114152849	0.0928982700643	0.0295729528535	0.215067615593	12.1704615032	-39.8278554496	43.3542168025
24	0.0559285783336	-0.0260308547984	0.0623590203078	0.0314164502481	0.00125844537416	0.0085448501077	-0.0541421913271	0.0333822591861	-0.00363288325723	-0.116786536459	0.0335743632546	-0.142989239809	0.00468923208972	0.0646917386394	-1.05897714822E-5	0.12823126795	-0.00377070690857	0.0196740786239	0.111722577972	0.00477357372244	0.13144641516	13.9648961282	-49.3010248165	44.3328576015
25	0.117790316122	-0.101278325861	0.064405230201	0.0425369543354	-0.0394753937012	0.0285323899717	0.0158262101718	-0.0243267586988	-0.0453245442315	-0.0512792830542	-0.0123308055651	0.0190691545554	-0.00886777926051	0.00937281165214	-0.00217624755868	0.0883257157623	-0.00369178805205	0.00984037450846	0.0717308374559	-0.00558209359872	0.117690521769	3.57580844907	-58.9828485749	49.9838429296

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 92 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 93 through 171 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 172 through 239 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -2 through 35 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 36 through 92 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 93 through 171 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 172 through 239 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid -2 through 18 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 19 through 45 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 46 through 78 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 79 through 154 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 155 through 184 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 185 through 217 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 218 through 239 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid -2 through 29 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 30 through 56 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 57 through 78 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 79 through 105 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 106 through 119 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 120 through 142 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 143 through 184 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 185 through 198 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 199 through 217 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 218 through 239 )

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