PDB-8zfw: norbelladine 4'-O-methyltransferase S52T Y186F complexed with Mg ...

ID or keywords:

Entry

Database: PDB / ID: 8zfw

Title

norbelladine 4'-O-methyltransferase S52T 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: 2.18 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	May 8, 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	8zfw.cif.gz	250.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8zfw.ent.gz		Display	PDB format
PDBx/mmJSON format	8zfw.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/zf/8zfw ftp://data.pdbj.org/pub/pdb/validation_reports/zf/8zfw	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 8z8sC 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

55.6 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)	80.501, 116.587, 50.297
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

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Protein , 1 types, 2 molecules AB

#1: Protein	Norbelladine 4'-O-methyltransferase / NpN4OMT Mass: 27183.893 Da / Num. of mol.: 2 / Mutation: S52T/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

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Non-polymers , 5 types, 139 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / 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-A1LU2 / Norbelladine Mass: 259.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₁₇NO₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.17 Å³/Da / Density % sol: 43.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 12% (w/v) PEG 8000, 0.2M MgCl2, 0.1M Tris-HCl (pH 9.0)

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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: 2.18→47.21 Å / Num. obs: 47598 / % possible obs: 100 % / Redundancy: 8.2 % / B_iso Wilson estimate: 38.73 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.088 / Net I/σ(I): 17
Reflection shell	Resolution: 2.18→2.25 Å / Redundancy: 8.6 % / R_merge(I) obs: 0.943 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2153 / CC_1/2: 0.758 / % 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: 2.18→47.21 Å / SU ML: 0.2572 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1532
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2135	3736	7.85 %
R_work	0.1753	43862	-
obs	0.1784	47598	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: 47.41 Å²

Refinement step

Cycle: LAST / Resolution: 2.18→47.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3792	0	31	132	3955

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0037	4022
X-RAY DIFFRACTION	f_angle_d	0.6735	5476
X-RAY DIFFRACTION	f_chiral_restr	0.0461	613
X-RAY DIFFRACTION	f_plane_restr	0.0038	697
X-RAY DIFFRACTION	f_dihedral_angle_d	23.6871	1485

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 (%)
2.18-2.21	0.3538	136	0.302	1599	X-RAY DIFFRACTION	100
2.21-2.24	0.3015	137	0.2814	1628	X-RAY DIFFRACTION	99.94
2.24-2.27	0.3649	137	0.2787	1612	X-RAY DIFFRACTION	100
2.27-2.3	0.2815	142	0.2465	1676	X-RAY DIFFRACTION	100
2.3-2.33	0.2809	138	0.2336	1572	X-RAY DIFFRACTION	99.82
2.33-2.37	0.2872	142	0.2335	1672	X-RAY DIFFRACTION	99.89
2.37-2.41	0.2344	139	0.225	1610	X-RAY DIFFRACTION	100
2.41-2.45	0.2792	139	0.2196	1609	X-RAY DIFFRACTION	99.94
2.45-2.5	0.2793	145	0.2108	1654	X-RAY DIFFRACTION	99.89
2.5-2.54	0.2886	138	0.2165	1625	X-RAY DIFFRACTION	100
2.54-2.6	0.2516	134	0.2012	1629	X-RAY DIFFRACTION	99.94
2.6-2.65	0.2608	136	0.1999	1649	X-RAY DIFFRACTION	99.94
2.65-2.71	0.2207	135	0.1801	1591	X-RAY DIFFRACTION	99.83
2.71-2.78	0.2186	143	0.1908	1644	X-RAY DIFFRACTION	99.5
2.78-2.86	0.2389	135	0.1952	1600	X-RAY DIFFRACTION	99.43
2.86-2.94	0.2334	139	0.1964	1622	X-RAY DIFFRACTION	99.38
2.94-3.04	0.239	136	0.1867	1596	X-RAY DIFFRACTION	98.63
3.04-3.14	0.2288	143	0.194	1652	X-RAY DIFFRACTION	98.95
3.14-3.27	0.2041	139	0.1758	1591	X-RAY DIFFRACTION	99.71
3.27-3.42	0.1894	135	0.1579	1642	X-RAY DIFFRACTION	100
3.42-3.6	0.1909	135	0.1659	1619	X-RAY DIFFRACTION	100
3.6-3.82	0.2191	144	0.1504	1619	X-RAY DIFFRACTION	100
3.82-4.12	0.1838	130	0.1416	1641	X-RAY DIFFRACTION	100
4.12-4.53	0.1817	142	0.124	1636	X-RAY DIFFRACTION	100
4.53-5.19	0.1593	140	0.1478	1602	X-RAY DIFFRACTION	100
5.19-6.53	0.2188	138	0.172	1638	X-RAY DIFFRACTION	100
6.54-47.21	0.1635	139	0.1604	1634	X-RAY DIFFRACTION	99.72

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	1.94232082069	-1.343332551	-0.38359266204	3.1997059919	1.24743629114	0.714167295723	-0.040695318779	-0.18162996362	-0.263132172355	0.421619825038	-0.0628558939892	-0.459456315266	0.256946300944	0.134534211767	0.134831333517	0.385495491048	-0.000325432180292	-0.0199833129446	0.407631144508	0.0462986669369	0.367888746136	38.6586614029	26.1907286596	28.1674884146
2	1.91392668632	0.045043852201	0.285144267201	3.79795913247	-1.35437673061	1.75393159928	0.174269000803	-0.515372292455	0.0930585093968	0.725599398826	-0.20536606993	0.0908474104668	0.110859042373	-0.0394426897509	-0.121886846415	0.401985187998	-0.0818649863399	-0.0147082713738	0.408416745221	-0.0060909169226	0.308752317686	23.973565328	23.0944974913	34.7664678299
3	2.71986721632	-0.438716856125	0.650530688435	2.18419343084	-0.633710163499	2.673696378	0.163079322902	-0.0903696694643	-0.336358931179	0.0972893897016	-0.0967087103237	-0.1119306732	0.123314433667	0.173565064987	-0.115659842863	0.250320880334	-0.0316466017768	-0.0104008616924	0.268040505474	-0.0199493471779	0.303929691826	26.4175412102	20.2753597282	24.9451444551
4	3.12369267527	-1.21586011602	1.89309450527	1.44178251852	-0.88634493872	3.65069299236	-0.0233118162236	0.101265962619	-0.329600529151	-0.0993721870415	-0.0504922185059	0.00242315959581	0.119580926706	-0.430420855103	0.0773438097276	0.328277401834	-0.0346755909727	0.0299415905556	0.394752624788	-0.0814287724719	0.523253201639	19.6711341236	12.7575568803	21.1300251075
5	1.13924040451	0.314215623334	0.335167771928	0.912860089643	0.422230845474	1.63997055878	0.148950241936	-0.29154057148	-0.320306667575	0.025298612302	-0.0533247209548	0.373783154926	0.26013200908	-0.267027180377	-0.0436502381775	0.296386126911	-0.0573561776181	-0.0102281285713	0.297336266376	-0.0076964427921	0.424404364433	16.8229340154	13.9254043141	24.1601374808
6	4.28657244992	-0.79693573189	0.192655642958	2.472737583	0.0605458261815	2.23353248902	0.198867467899	-0.192844148889	-0.173130037035	0.793028747093	-0.339894290947	0.26955475361	0.00562516073302	-0.312119127256	0.00725506638559	0.547452290061	-0.144077720756	0.0939293179955	0.429624326524	0.0639333786113	0.348603339303	19.4481224323	10.2453538514	34.773824641
7	1.98250383159	-1.24881419052	-0.559623333418	2.45473765848	-0.114916199622	1.10835962431	-0.0667214610985	0.311930749398	-0.843051880792	-0.298985440567	-0.0802838927684	0.726539960519	0.329282512931	-0.244319800915	0.167073314131	0.378515007381	-0.103508308928	-0.0294670752727	0.40048221711	-0.0565215924114	0.631086237903	17.5472728109	3.74364485388	20.2055216539
8	4.76117420192	-0.657915636476	0.425322499746	3.79716686733	-0.805887897499	2.41493852972	0.267510505718	0.0617504949734	-0.985904665036	-0.715114699341	-0.12212353366	0.444995389468	0.881235513743	-0.399768265037	-0.29633300467	0.524623022619	-0.0578874976503	-0.0195224464178	0.358154147315	-0.0773864882162	0.484184473653	18.8762429168	10.2380917392	13.2367062519
9	1.41190496758	0.866689761477	-0.0316299004804	2.18260265378	0.291761731833	1.14247737566	-0.0416089966976	0.146304884379	-0.296016167238	-0.304321998476	0.00844972387332	-0.275061614108	0.203969959509	0.0329902888519	0.0466297374058	0.341417713101	0.0333755571143	0.0113515616609	0.302553114378	-0.0788447313367	0.32615465609	34.0928079416	13.8046036196	11.8939995721
10	1.17046168455	-0.247812283691	-0.442046190512	3.11304474166	-0.338590468051	1.8666716332	0.0016558107203	0.342250394545	0.116351650196	-0.525575666877	-0.0767041787378	-0.0348154655504	-0.113423970032	0.0428909284161	0.0693460430526	0.374245183684	-0.0048218900414	-0.00429181384116	0.333231341147	-0.00315292965062	0.226682992646	29.0139900256	38.6072958107	4.19047894522
11	1.44531443795	-0.283603539895	0.432510619335	1.89996994464	-0.441134453174	0.980023401836	0.019339773947	0.0128677195983	0.176149890693	-0.0118788056649	-0.0273315515865	-0.0455335751312	-0.0681154370575	0.0297611754401	0.0149805481853	0.266458167333	0.00876435703135	0.0276290919874	0.277288597204	-0.0334308784105	0.292707586882	26.0454437183	41.9795637796	20.091688138

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 29 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 30 through 46 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 70 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 71 through 83 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 84 through 105 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 106 through 118 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 119 through 142 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 143 through 157 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 158 through 239 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 6 through 157 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 158 through 239 )

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