PDB-8z8t: norbelladine 4'-O-methyltransferase S52T Y186F complexed with Mg ...

ID or keywords:

Entry

Database: PDB / ID: 8z8t

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: To Be Published
Title: Structural guided studies for Amaryllidaceae O-methyltransferases
Authors: Saw, Y.Y.H. / Nakashima, Y. / Morita, H.

History

Deposition	Apr 22, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 23, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8z8t.cif.gz	247.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8z8t.ent.gz		Display	PDB format
PDBx/mmJSON format	8z8t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/8z8t ftp://data.pdbj.org/pub/pdb/validation_reports/z8/8z8t	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Norbelladine 4'-O-methyltransferase

B: Norbelladine 4'-O-methyltransferase

hetero molecules

56.1 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

-
Protein , 1 types, 2 molecules AB

#1: Protein	Norbelladine 4'-O-methyltransferase / NpN4OMT Mass: 27395.109 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

-
Non-polymers , 5 types, 141 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 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.: 134 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.89 %
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)

-
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: 47597 / % 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

-
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: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.5284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2099	3735	7.85 %
R_work	0.1782	43862	-
obs	0.1808	47597	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: 47.39 Å²

Refinement step

Cycle: LAST / Resolution: 2.18→47.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3792	0	31	134	3957

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0027	3964
X-RAY DIFFRACTION	f_angle_d	0.5758	5396
X-RAY DIFFRACTION	f_chiral_restr	0.0442	603
X-RAY DIFFRACTION	f_plane_restr	0.0035	687
X-RAY DIFFRACTION	f_dihedral_angle_d	23.6751	1463

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	0.3593	136	0.3069	1599	X-RAY DIFFRACTION	100
2.21-2.24	0.3014	137	0.2888	1628	X-RAY DIFFRACTION	99.94
2.24-2.27	0.357	137	0.2863	1612	X-RAY DIFFRACTION	100
2.27-2.3	0.2823	142	0.2535	1676	X-RAY DIFFRACTION	100
2.3-2.33	0.2776	138	0.2411	1572	X-RAY DIFFRACTION	99.82
2.33-2.37	0.2848	142	0.2414	1672	X-RAY DIFFRACTION	99.89
2.37-2.41	0.239	139	0.2362	1610	X-RAY DIFFRACTION	100
2.41-2.45	0.2652	139	0.2273	1609	X-RAY DIFFRACTION	99.94
2.45-2.5	0.2709	145	0.2185	1654	X-RAY DIFFRACTION	99.89
2.5-2.54	0.2747	138	0.2214	1625	X-RAY DIFFRACTION	100
2.54-2.6	0.2509	134	0.2078	1629	X-RAY DIFFRACTION	99.94
2.6-2.65	0.26	136	0.2102	1649	X-RAY DIFFRACTION	99.94
2.65-2.71	0.2273	135	0.1902	1591	X-RAY DIFFRACTION	99.83
2.71-2.78	0.2298	143	0.2014	1644	X-RAY DIFFRACTION	99.5
2.78-2.86	0.2341	135	0.2052	1600	X-RAY DIFFRACTION	99.43
2.86-2.94	0.2274	139	0.2025	1622	X-RAY DIFFRACTION	99.38
2.94-3.04	0.2375	136	0.1887	1596	X-RAY DIFFRACTION	98.63
3.04-3.14	0.237	143	0.2001	1652	X-RAY DIFFRACTION	98.95
3.14-3.27	0.1955	139	0.1834	1591	X-RAY DIFFRACTION	99.71
3.27-3.42	0.188	135	0.1637	1642	X-RAY DIFFRACTION	100
3.42-3.6	0.1948	135	0.1688	1619	X-RAY DIFFRACTION	100
3.6-3.82	0.2205	144	0.154	1619	X-RAY DIFFRACTION	100
3.82-4.12	0.1864	130	0.1448	1641	X-RAY DIFFRACTION	100
4.12-4.53	0.1665	142	0.1273	1636	X-RAY DIFFRACTION	100
4.53-5.19	0.1617	140	0.1449	1602	X-RAY DIFFRACTION	100
5.19-6.53	0.2143	138	0.1705	1638	X-RAY DIFFRACTION	100
6.54-47.21	0.1434	138	0.1492	1634	X-RAY DIFFRACTION	99.66

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	0.357248849399	0.149711077144	0.0526453763317	0.342880590778	0.324136794952	0.338818852428	0.0503253599612	-0.028474935757	-0.105422836689	0.30241896264	-0.213929844509	-0.232068636088	0.141260498129	-0.00388986893769	-0.000108791261708	0.394971687999	-0.00162794618117	-0.0213569134682	0.414255639798	0.0446286345332	0.372028588867	38.6625403614	26.1809251059	28.1730802137
2	0.136581062031	0.290526043954	-0.00343274154405	0.643389501171	0.0970520582353	0.250232608523	0.275835896112	-0.413902963427	0.278987302854	0.602615641253	-0.052743551646	0.444442046995	-0.17834116481	-0.318345075405	0.00866083640766	0.347108284165	-0.104982755941	-0.0274575310391	0.348799264538	-0.00967516146054	0.260585673857	23.9769718993	23.0845399305	34.7673996287
3	0.315416087138	0.226350361457	-0.20951634154	0.270647516332	0.0162331337569	0.278420980668	0.190167376748	-0.0203851247257	-0.402380701411	0.00295355665834	-0.0563771308825	-0.0602281240853	0.0895424555015	0.159423493497	-8.64556408442E-5	0.326685555654	-0.0208987822361	-0.0327553542632	0.351422637822	-0.0175876719106	0.37084990288	26.4178546408	20.2733022525	24.9510276996
4	0.154942369887	0.095505700052	-0.115721164285	0.0500765730984	0.0469546454414	0.152896143841	0.0512467793137	-0.161131361994	-0.27988146109	-0.017766636759	-0.0322023618072	0.0904360169044	0.0860227993956	-0.561968785269	0.00029318942961	0.360177284178	-0.00803993459057	0.0213942979153	0.423758787952	-0.0699954658374	0.519256840474	19.6764220789	12.7595393009	21.1285046838
5	0.0499991618865	-0.114875892314	-0.104744598886	0.122773380496	0.139585881393	0.0605181693014	0.14352692977	-0.254332144283	-0.0204546610687	0.133208896552	-0.0731094489305	0.131553784196	0.191010121253	-0.213128847871	3.28929402158E-5	0.298413719081	-0.0422636492273	-0.0200975737553	0.281627165466	-0.0196895019313	0.424226502006	16.8265632923	13.9208188594	24.1629085232
6	0.033795470353	0.00917369726275	0.03514692552	0.0123969836803	-0.0035515834634	0.0402414426873	0.189189694314	-0.234673425092	-0.101457709268	0.915456770127	-0.202955478135	-0.220008619165	0.175874563663	-0.0251680897539	0.000217704041392	0.570839241539	-0.100553162617	0.0944291208006	0.480052230445	0.0769789689438	0.437138419562	19.442629465	10.2456668111	34.7743397619
7	0.106471169314	0.0612080329024	-0.0323849389523	0.395552682931	-0.362499696769	0.341709317897	-0.144410470821	0.00135180494493	-0.654865276219	0.0631037083353	0.0204733506428	0.717002309081	0.216818577033	-0.263032534809	-0.0109488293255	0.323467908541	-0.0950661106413	-0.0337385075787	0.335417343295	-0.0653122826203	0.605512927591	17.5551255982	3.74158846014	20.1998681684
8	0.135883899881	0.159469566343	-0.14850810608	0.120108773486	-0.136642219502	0.161664208019	0.357555670343	-0.253890866673	-0.69326974669	-0.309881900355	-0.0823183694148	0.259455599342	0.590888093912	-0.347926270611	-7.98711300466E-5	0.515293725212	-0.0389668280215	-0.0452558431663	0.430518612917	-0.0595739296214	0.547503901221	18.8835225412	10.2390701612	13.2343590413
9	0.724003735079	0.712141679021	-0.188486409042	1.47747530676	0.125227356549	0.546697757858	-0.0706489342861	0.0421440876892	-0.219296059076	-0.176741538778	0.0154527778437	-0.280318489203	0.137870148198	0.0660967395422	-3.79461332538E-5	0.369419235311	0.0374490704597	0.00791972606666	0.344033780307	-0.0828499991004	0.371194338467	34.101168023	13.8003819499	11.8995985224
10	0.350734006429	-0.0776269683334	-0.351935277533	2.1657835109	-0.245335426404	1.34174667882	-0.02036816668	0.228872387005	0.0712122879604	-0.456474470085	-0.0534938999412	-0.0217291864316	-0.0800704540115	0.0710982705103	4.19564248684E-5	0.40437847709	-0.00029042493944	-0.0120914056326	0.380947035408	0.00187705830858	0.278854007759	28.4009186977	38.5838843907	3.68795888715
11	0.520257302677	-0.410629909412	0.486416918734	1.1533365628	-0.566898011013	0.385011359234	0.0121719766896	0.0134221761967	0.129336253106	-0.0183335460441	-0.0282475421557	-0.0301941490628	-0.0443379011814	0.019520558505	-2.49278360068E-5	0.279840620661	0.00200268361056	0.0207002536219	0.300059988632	-0.0361921022077	0.321146532922	26.0501834968	41.9787123942	20.0838775024

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 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 141 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 141 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 141 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi