PDB-8z8s: norbelladine 4'-O-methyltransferase S52M Y186F complexed with Mg ...

ID or keywords:

Entry

Database: PDB / ID: 8z8s

Title

norbelladine 4'-O-methyltransferase S52M 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: 1.94 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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PDBx/mmCIF format	8z8s.cif.gz	244.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8z8s.ent.gz	162.6 KB	Display	PDB format
PDBx/mmJSON format	8z8s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8z8s_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8z8s_full_validation.pdf.gz	1.9 MB	Display
Data in XML	8z8s_validation.xml.gz	21 KB	Display
Data in CIF	8z8s_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/8z8s ftp://data.pdbj.org/pub/pdb/validation_reports/z8/8z8s	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 8z8pC 8z8rC 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

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)	80.588, 116.779, 50.079
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	Norbelladine 4'-O-methyltransferase / NpN4OMT Mass: 27425.201 Da / Num. of mol.: 2 / Mutation: S52M, 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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: 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
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 203 / 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: 42.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 23% (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: 1.94→47.28 Å / Num. obs: 65279 / % possible obs: 98.6 % / Redundancy: 7.5 % / B_iso Wilson estimate: 29.9 Å² / CC_1/2: 0.973 / R_merge(I) obs: 0.189 / Net I/σ(I): 7.2
Reflection shell	Resolution: 1.94→1.99 Å / Redundancy: 8.1 % / R_merge(I) obs: 1.402 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2334 / CC_1/2: 0.704 / % possible all: 98.2

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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: 1.94→47.28 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.4494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2694	3696	5.66 %
R_work	0.2383	61583	-
obs	0.2401	65279	96.54 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.94→47.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3790	0	6	203	3999

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0048	3939
X-RAY DIFFRACTION	f_angle_d	0.6983	5365
X-RAY DIFFRACTION	f_chiral_restr	0.0485	602
X-RAY DIFFRACTION	f_plane_restr	0.0045	687
X-RAY DIFFRACTION	f_dihedral_angle_d	21.6765	1458

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 (%)
1.94-1.97	0.3898	140	0.3606	2345	X-RAY DIFFRACTION	95.91
1.97-1.99	0.3702	140	0.3557	2391	X-RAY DIFFRACTION	97.35
1.99-2.02	0.4436	141	0.3575	2387	X-RAY DIFFRACTION	96.64
2.02-2.05	0.3826	144	0.3337	2378	X-RAY DIFFRACTION	97.11
2.05-2.08	0.3966	143	0.3399	2405	X-RAY DIFFRACTION	97.55
2.08-2.12	0.3038	143	0.306	2399	X-RAY DIFFRACTION	96.73
2.12-2.15	0.3553	139	0.3076	2365	X-RAY DIFFRACTION	97.81
2.15-2.19	0.342	144	0.3017	2370	X-RAY DIFFRACTION	97.14
2.19-2.24	0.3408	142	0.29	2380	X-RAY DIFFRACTION	97.07
2.24-2.28	0.325	150	0.2874	2435	X-RAY DIFFRACTION	97.95
2.28-2.33	0.2558	144	0.2779	2343	X-RAY DIFFRACTION	97.22
2.33-2.38	0.3046	144	0.275	2412	X-RAY DIFFRACTION	96.71
2.38-2.44	0.2904	139	0.2616	2384	X-RAY DIFFRACTION	97.3
2.44-2.51	0.2991	144	0.2559	2374	X-RAY DIFFRACTION	96.96
2.51-2.58	0.3456	143	0.264	2340	X-RAY DIFFRACTION	96.73
2.58-2.67	0.3302	145	0.2621	2363	X-RAY DIFFRACTION	96.09
2.67-2.76	0.2491	143	0.2616	2362	X-RAY DIFFRACTION	95.79
2.76-2.87	0.3387	144	0.2589	2294	X-RAY DIFFRACTION	94.28
2.87-3	0.3155	126	0.2496	2259	X-RAY DIFFRACTION	91.55
3-3.16	0.3204	138	0.2523	2269	X-RAY DIFFRACTION	92.33
3.16-3.36	0.2862	145	0.2326	2344	X-RAY DIFFRACTION	95.66
3.36-3.62	0.237	145	0.2278	2414	X-RAY DIFFRACTION	98.42
3.62-3.98	0.217	145	0.2026	2399	X-RAY DIFFRACTION	97.85
3.99-4.56	0.196	138	0.1842	2403	X-RAY DIFFRACTION	97.02
4.56-5.74	0.183	143	0.1793	2365	X-RAY DIFFRACTION	97.25
5.75-47.28	0.2135	144	0.1747	2403	X-RAY DIFFRACTION	97.85

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	0.00691545738652	-0.0739325227482	0.125673603643	0.227197436103	-0.130265466098	-0.00367282236343	0.085145722701	-0.101916342382	-0.14733493355	0.115397790487	-0.118708328714	0.0496710555857	-0.0292714670766	0.0789638020709	0.000657659525903	0.232960031493	-0.0103823374903	-0.00229595004445	0.291359806694	0.0127015339135	0.266778408461	35.273517295	26.8481243467	28.705126726
2	0.712499073089	0.30550693833	-0.25297947888	1.18610812102	-0.209301923428	0.812692826381	0.0757315627018	-0.0339864666697	-0.139137489123	-4.5234829107E-5	-0.0933787290618	0.185719525822	0.121408913538	-0.108044784601	-0.000172741004788	0.253776173918	-0.0383055237709	-0.0137235620477	0.247034697076	-0.00402203895191	0.279470794672	20.5433137548	12.9358804161	23.8401029213
3	0.657221000319	0.788947982369	-0.551307419781	0.833615563256	-0.263453352283	0.467326499087	-0.106766390978	0.0070226216505	-0.200157553952	-0.20877417566	0.0580242094673	-0.0800406253139	0.15273719245	0.0614291412699	-3.41872746549E-5	0.277193991724	0.0421530140113	0.00415738855706	0.241231237085	-0.0498231752696	0.273714916522	34.2915827444	13.8528983099	11.6830138151
4	0.465661624529	0.00162681649629	-0.0632473207659	1.02715213635	0.317022088367	0.495692858073	-0.0773438661997	-0.035138549482	0.159866389321	-0.227342440707	-0.0214794698678	-0.115347347125	-0.286605941364	0.0595994641702	0.00681266591169	0.311636049062	0.0333014017806	0.0450894545893	0.320346160556	0.0464478458354	0.420639885134	44.1227894321	33.3714191467	13.0824224523
5	0.499483086086	-0.109406548824	-0.419963097245	0.372048459072	0.00753942269524	0.94678829597	-0.023102737388	0.165481418951	0.124699207618	-0.140534913372	0.0279774936335	0.116950323966	-0.0921738254885	-0.0339722238166	1.97859924242E-5	0.283967463709	0.00269454860718	-0.0134429168822	0.281637549315	0.00749111557866	0.250924825883	25.8033957317	39.5762811039	1.67209431393
6	0.179347394705	0.0738518887111	0.0960128001518	0.327332121196	-0.435266410006	0.334877229875	0.015788775797	0.112618070745	0.135385886101	0.0587355093995	-0.0648048057998	-0.0689632544102	-0.0450043483297	0.0142769299564	-3.9928228649E-5	0.234094765378	0.00664291499071	0.0199241375491	0.238018246046	-0.00527917195281	0.223106595714	27.3796533858	43.576319844	18.5633894895
7	0.259847702712	-0.318925008266	0.139814759907	0.334158940377	-0.36849127541	0.0516125168661	0.0195200251503	-0.0081359241545	0.149245706088	0.0143409138049	-0.00716051839402	0.0350874920016	-0.082254351848	-0.0490415315063	4.38990806923E-5	0.248684180395	0.00125974742033	0.0232239261047	0.252130106036	-0.0184201734615	0.27285235964	25.2981789604	40.2727350203	21.6683951092

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 157 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 158 through 239 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 6 through 29 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 30 through 157 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 158 through 198 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 199 through 239 )

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