PDB-8z8p: norbelladine 4'-O-methyltransferase S52M variant complexed with M...

ID or keywords:

Entry

Database: PDB / ID: 8z8p

Title

norbelladine 4'-O-methyltransferase S52M variant 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: 1.68 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	8z8p.cif.gz	506.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8z8p.ent.gz	343.6 KB	Display	PDB format
PDBx/mmJSON format	8z8p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8z8p_validation.pdf.gz	4.7 MB	Display	wwPDB validaton report
Full document	8z8p_full_validation.pdf.gz	4.7 MB	Display
Data in XML	8z8p_validation.xml.gz	47.7 KB	Display
Data in CIF	8z8p_validation.cif.gz	70.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/8z8p ftp://data.pdbj.org/pub/pdb/validation_reports/z8/8z8p	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 8z8oC 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
56.1 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
56 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.494, 79.948, 91.634
Angle α, β, γ (deg.)	90.000, 93.725, 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: 27441.201 Da / Num. of mol.: 4 / Mutation: S52M 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.: 7 / 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.: 1024 / 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: 42.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 26% (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: 1.035 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: 1.68→45.72 Å / Num. obs: 105592 / % possible obs: 99.8 % / Redundancy: 4.3 % / B_iso Wilson estimate: 16.88 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.071 / Net I/σ(I): 12.1
Reflection shell	Resolution: 1.68→1.71 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.567 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5229 / CC_1/2: 0.735 / % possible all: 99.3

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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: 1.68→45.72 Å / SU ML: 0.151 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.179	2000	1.89 %
R_work	0.1564	103570	-
obs	0.1569	105570	99.79 %

Solvent computation

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

Displacement parameters

B_iso mean: 23.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→45.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7753	0	42	1024	8819

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	8182
X-RAY DIFFRACTION	f_angle_d	0.9272	11145
X-RAY DIFFRACTION	f_chiral_restr	0.0562	1241
X-RAY DIFFRACTION	f_plane_restr	0.0053	1429
X-RAY DIFFRACTION	f_dihedral_angle_d	20.7399	3053

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 (%)
1.68-1.72	0.2489	138	0.2189	7361	X-RAY DIFFRACTION	99.48
1.72-1.77	0.2058	139	0.2106	7352	X-RAY DIFFRACTION	99.53
1.77-1.82	0.2306	139	0.2066	7320	X-RAY DIFFRACTION	99.53
1.82-1.88	0.2266	141	0.1981	7373	X-RAY DIFFRACTION	99.77
1.88-1.95	0.214	147	0.1779	7403	X-RAY DIFFRACTION	99.81
1.95-2.02	0.231	148	0.17	7348	X-RAY DIFFRACTION	99.91
2.02-2.12	0.1788	134	0.1616	7360	X-RAY DIFFRACTION	99.96
2.12-2.23	0.2268	141	0.1564	7428	X-RAY DIFFRACTION	99.92
2.23-2.37	0.1781	149	0.1516	7393	X-RAY DIFFRACTION	99.91
2.37-2.55	0.1846	142	0.1565	7393	X-RAY DIFFRACTION	99.92
2.55-2.81	0.1724	147	0.1533	7398	X-RAY DIFFRACTION	99.74
2.81-3.21	0.1705	148	0.1533	7464	X-RAY DIFFRACTION	99.96
3.21-4.05	0.1525	140	0.1314	7433	X-RAY DIFFRACTION	99.89
4.05-45.72	0.143	147	0.141	7544	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	0.0150242972897	0.0343740200554	-0.030101399065	0.0665188932348	-0.0198921439674	0.0393531089087	-0.14679973928	-0.0909207787797	0.0749646439248	0.20754382207	0.0734498122609	-0.0322673644126	0.0387001216652	0.130463414308	-6.19260312593E-5	0.214797305299	-0.00893707423719	-0.0378277902412	0.198714452088	-0.0246623368365	0.285979980079	7.3700036682	3.48620632845	47.114022382
2	0.144518244342	-0.00576358049248	0.00771512344845	0.0479912093798	-0.0302707887999	0.0333664147704	-0.0728295003403	-0.0741140009592	0.0198407112442	0.257435057771	-0.0111020059289	0.0649321592418	-0.0391113087583	-0.0170850099231	-0.00861126343652	0.132231333154	0.0066082062203	-0.0242984747271	0.117978089653	-0.00729471396144	0.10902127075	-4.61639402932	-9.9722823274	50.926334933
3	0.738091844575	-0.1023529907	-0.201856380399	0.166993374835	-0.154129034654	0.130739619114	-0.000686575774325	-0.0621345544444	-0.0155336945561	0.039397611404	0.0202172478464	-0.0649143234927	0.0116948287152	0.0154911656151	0.000888666713825	0.11461693706	0.0011214361869	-0.0134725565068	0.105490705189	-0.0041304490952	0.115871310451	7.80053902527	-16.135838625	45.164864394
4	0.176166966724	-0.164679867251	-0.00255864141752	0.165185056662	0.0603885252819	0.00749960166201	-0.122245333616	-0.0538322632955	-0.066995495034	0.0807286054539	0.10090476858	-0.0781745833375	0.0557530265844	0.0514957930421	-0.0119559711761	0.146175534306	0.00762292310793	-0.0212985610841	0.14006392503	0.00440634771763	0.150482726485	16.1768332063	-21.6784090719	46.9057133765
5	0.119687229657	-0.0392394209296	0.0113492514177	0.0696072636632	0.0328255840079	0.0984886303288	0.00179198049026	0.0943294581009	-0.116927368022	0.092291898592	0.00620987487903	-0.0922133451617	0.0753547203949	0.135539853922	0.00173722115183	0.114326967222	0.00396828938466	-0.00204150088734	0.153350775772	-0.000526146805937	0.160668882155	21.245787079	-21.625997232	37.1034783938
6	0.491025607871	-0.208483103113	0.292202956809	0.0947908538473	-0.123933860549	0.239701643947	0.00839956302936	0.291908495746	-0.063871347041	-0.0622611027703	-0.104666232353	-0.110162567674	0.0365554237321	0.188980619196	-0.00918815070739	0.104677599264	-0.00720682127782	0.0103868740467	0.181034544261	0.0150478204671	0.148270072491	15.751253196	-15.8906536701	29.6361788714
7	0.639848837793	-0.454009804108	-0.0454225670483	0.32493549498	-0.0575947134456	0.301275586724	0.00494826375066	0.128469318982	0.144447045502	-0.0209934662412	-0.0255961723416	-0.0995741001951	-0.0517963994276	0.0483579655526	-0.0350791015183	0.0967969112585	-0.0202916158651	0.00167258771042	0.110847690106	0.0238908872568	0.107332575378	8.52581556385	-4.40586219426	30.5825029367
8	0.0744298669393	0.0520097145253	0.0681617495023	0.1467340882	-0.0428860467315	0.0543151252243	-0.179093755129	0.252336404249	0.0658892866876	-0.0308908927881	0.150700390942	-0.232331526867	0.110393901751	0.00111295444957	0.000434725508976	0.26328867491	-0.0301070934973	0.0305200776525	0.217087362132	0.00181046402856	0.276355041428	37.4760061263	-1.51043871205	83.0950558877
9	0.186939586533	-0.0411130725421	-0.0944213721599	0.129050454782	0.233559577943	0.187929849301	-0.00568678636717	-0.0792706582836	0.0351274958495	0.0135842814541	0.108627290456	-0.0948654018002	-0.0500383951163	0.122209249402	0.011838899625	0.14276421722	-0.00309309479004	0.0152695441165	0.127908539166	-0.0269762380463	0.14033258663	35.1517950797	-14.4630850172	92.2058169574
10	0.16179541296	-0.103015955726	-0.00696602654492	0.0464921415789	-0.0144362943129	0.0367933862251	-0.121302381141	0.0304459863618	-0.0480079956309	-0.0964409214642	0.0636956309854	0.0198932688185	0.000571781317767	-0.0366413454309	-0.000257031316599	0.154759740272	-0.0201617095606	0.0138999642027	0.110552641905	0.000101453536763	0.120123683503	26.3424019789	-23.7496499027	80.5949359819
11	0.0832191332012	-0.0859636682768	-0.0608558435318	0.115140164358	0.036130120235	0.218660236569	-0.0989201608826	0.025551358466	-0.0739411716533	-0.0390093016709	0.128256977165	-0.135189158202	0.106112637186	0.0736826836743	0.0289494400231	0.144888053809	-0.00887265410271	0.0283548420618	0.109556468665	-0.0374724854905	0.170110353285	39.734929646	-24.3844216538	80.6263646982
12	0.103883283087	-0.0711438735785	0.0216328667703	0.119816708425	0.0664755917358	0.046903502021	-0.0397746174307	0.132701678366	-0.146537698328	-0.174688938976	0.0563677031531	-0.265286835898	0.200591224025	0.141394218771	0.000844936002357	0.219823875493	-0.0305245224682	0.0597819311539	0.17449806501	-0.0344505498427	0.182682563575	38.7581820159	-25.5115711869	68.9264057016
13	0.149339362205	-0.111548748135	0.0479667039255	0.036228231411	-0.00217699042086	-0.00797556705547	0.00915674643158	0.193233152787	-0.0776577177358	-0.0683807215716	0.111491943809	-0.199280464663	0.047548045163	0.0310075315953	0.00417123350551	0.197446084721	-0.0633913465978	0.0305273935945	0.169625240613	-0.0302942368131	0.150482525188	29.7503155802	-24.0229511917	68.5288514389
14	0.179832288625	-0.175694274499	0.0801915326757	0.129558612087	-0.15527918763	0.115851631671	-0.0167186450897	0.157878349012	0.0711540006206	-0.165908307289	0.0369528957257	-0.00589393270869	0.0378438795915	-0.0497899234931	0.00566194184919	0.198671328037	-0.0498039917917	0.0242088494137	0.182348823377	-0.00405841631063	0.102506727254	27.6564889702	-16.0445430675	68.4762866421
15	0.108152727929	-0.0715686689126	-0.158653246405	0.141059223756	0.0155815944355	0.208074484882	-0.00435458503915	0.169947558725	0.177019240237	-0.107864454712	0.0895918486089	-0.070348376268	-0.0980349501064	0.0166539521543	0.00222240336416	0.202794071872	-0.0331648488124	0.00864900459047	0.163522181036	0.0428029736251	0.165207955008	29.5647544387	0.327039928572	73.1474977938
16	0.0640282923402	-0.198943302007	0.037146223717	0.134519744445	-0.00260655764763	0.0551494863036	-0.00904598060518	0.105476210516	0.0423710266935	-0.0395967250412	0.0571496768276	-0.00657276848493	0.0154932095709	-0.0926880820072	0.030483386697	0.147241000729	-0.051532653366	-0.00868407806882	0.169145688963	0.0149787958536	0.0823090075	19.5268795528	-14.7500650511	71.9783959976
17	0.913370752462	0.00566652182947	-0.17839196609	0.36845699392	-0.204543349311	0.709208334885	-0.0352718827593	0.102453807933	0.00293138064126	-0.0178039073407	0.100059920609	0.119200111321	-0.0180710980005	-0.173458801517	0.013562160117	0.121762016321	-0.00467214286487	-0.0041819793017	0.182003252702	0.0516471608542	0.147499281026	3.52767209491	-13.7829694118	84.9826545499
18	0.312210538684	0.113672278454	0.0373825528592	0.0375815348717	0.0361087733946	0.205725733789	0.0227288027022	-0.0140278997819	0.0110831531619	0.0579443510985	0.00328892773334	0.0426154762232	0.00336849619701	-0.0736645182513	-0.00457785742412	0.156573176483	0.00582482191818	0.027148246106	0.10846616132	0.0193921635246	0.12049469674	13.6282826267	-16.9593257632	97.7164668954
19	0.103217505527	0.166466630759	0.0361236241281	0.158767508795	-0.00831545198308	0.210041935848	-0.0494846833935	-0.191558757455	0.173749495935	-0.0524648230925	0.0256366392854	-0.133578340311	-0.0123619569658	0.165845984972	-1.52024327531E-5	0.153914028147	-0.00376435907854	0.000745104050883	0.174013985914	-0.0170884853422	0.21719838782	5.8973644127	-36.743091672	56.804268225
20	1.50093989978	-0.338473921766	-0.122805789618	0.472431712263	0.280242801537	0.407078076067	-0.0576219193342	-0.30688488862	-0.0133252521405	0.0674962241608	0.0891118273507	-0.119855643036	0.0273365051885	0.0637365232849	-0.110367048002	0.112079371964	0.00873988680372	-0.0256680944523	0.185043903567	0.00112492924662	0.11407979296	11.3427443153	-54.9912213668	65.6059285361
21	0.549814135035	-0.106445468443	0.317472300275	0.114671171807	-0.0768663507101	-0.126524805547	-0.0241002915611	0.0212020350594	0.0260240003144	-0.0468845387112	-0.00617218885608	-0.0297069551475	0.001449306292	0.0244614787698	-6.23873285363E-5	0.116033275924	-0.00734450570879	0.0101244118831	0.0824499979348	-0.00117025132681	0.108057834701	9.04842740443	-51.8916793033	47.9813977959

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 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 92 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 93 through 118 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 119 through 142 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 143 through 171 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 172 through 239 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid -2 through 18 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 19 through 56 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 57 through 78 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 79 through 118 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 119 through 142 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 143 through 157 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 158 through 184 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 185 through 217 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 218 through 239 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid -2 through 154 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 155 through 239 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid -2 through 29 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 30 through 171 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 172 through 239 )

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