PDB-9p2u: Structure of radical S-adenosylmethionine methyltransferase, NocN...

ID or keywords:

Entry

Database: PDB / ID: 9p2u

Title

Structure of radical S-adenosylmethionine methyltransferase, NocN, from Nocardia with two AzaSAM and [4Fe-4S] cluster bound

Components

Radical S-adenosylmethionine methyltransferase NocN

Keywords

OXIDOREDUCTASE / radical S-adenosylmethionine enzyme nocathiacin nosiheptide

Function / homology

Function and homology information

porphyrin-containing compound biosynthetic process / catalytic activity / 4 iron, 4 sulfur cluster binding / cytoplasm
Similarity search - Function

Biological species

Nocardia sp. ATCC 202099 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.4 Å

Authors

Wang, B. / Knox, H.L. / York, N.J. / Radle, M.I. / Silakov, A. / Booker, S.J.

Funding support

United States, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2026
Title: Structural and Spectroscopic Basis for Catalysis by a Class C Radical S-Adenosylmethionine Methylase Involved in Nosiheptide/Nocathiacin Biosynthesis
Authors: Wang, B. / Knox, H.L. / York, N.J. / Radle, M.I. / Silakov, A. / Booker, S.J.

History

Deposition	Jun 12, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 3, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9p2u.cif.gz	201.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9p2u.ent.gz	157.1 KB	Display	PDB format
PDBx/mmJSON format	9p2u.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/p2/9p2u ftp://data.pdbj.org/pub/pdb/validation_reports/p2/9p2u	HTTPS FTP

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Related structure data

Related structure data	9p3bC 9p3cC 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: Radical S-adenosylmethionine methyltransferase NocN

hetero molecules

47.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	46.551, 70.506, 54.672
Angle α, β, γ (deg.)	90.00, 97.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Radical S-adenosylmethionine methyltransferase NocN / Heme chaperone HemW Mass: 46377.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nocardia sp. ATCC 202099 (bacteria) / Gene: nocN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5DUI5
#2: Chemical	ChemComp-SA8 / S-5'-AZAMETHIONINE-5'-DEOXYADENOSINE / 5'-[N-[(3S)-3-AMINO-3-CARBOXYPROPYL]-N-METHYLAMINO]-5'-DEOXYADENOSINE Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.98 Å³/Da / Density % sol: 37.97 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 200 mM Ca(OAc)2, 20% w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.99999 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 23, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.99999 Å / Relative weight: 1

Reflection

Resolution: 1.4→50 Å / Num. obs: 119219 / % possible obs: 96.7 % / Redundancy: 3.9 % / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.036 / R_pim(I) all: 0.02 / R_rim(I) all: 0.041 / Χ²: 0.785 / Net I/σ(I): 24.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.4-1.42	2.4	0.143	2503	0.952	0.988	0.114	0.185	0.695	73.1
1.42-1.45	2.6	0.128	2778	0.962	0.99	0.098	0.162	0.708	81.1
1.45-1.48	2.8	0.114	3036	0.968	0.992	0.082	0.141	0.799	88.2
1.48-1.51	3	0.102	3283	0.976	0.994	0.068	0.123	0.782	95.2
1.51-1.54	3.6	0.094	3394	0.984	0.996	0.056	0.11	0.829	99.7
1.54-1.58	4.1	0.08	3415	0.989	0.997	0.045	0.092	0.799	100
1.58-1.62	4.1	0.072	3442	0.99	0.998	0.04	0.082	0.782	100
1.62-1.66	4.1	0.062	3472	0.993	0.998	0.034	0.071	0.746	100
1.66-1.71	4.1	0.055	3416	0.994	0.998	0.03	0.063	0.729	100
1.71-1.76	4.1	0.05	3462	0.993	0.998	0.027	0.057	0.727	100
1.76-1.83	4.2	0.046	3412	0.995	0.999	0.025	0.053	0.73	100
1.83-1.9	4.1	0.043	3436	0.995	0.999	0.024	0.05	0.8	100
1.9-1.99	4.1	0.045	3439	0.995	0.999	0.025	0.051	1.117	100
1.99-2.09	4.2	0.035	3452	0.996	0.999	0.019	0.04	0.698	100
2.09-2.22	4.2	0.034	3454	0.996	0.999	0.019	0.039	0.712	100
2.22-2.39	4.1	0.038	3438	0.995	0.999	0.021	0.044	0.98	100
2.39-2.63	4.2	0.036	3467	0.996	0.999	0.02	0.041	0.801	100
2.63-3.02	4.2	0.04	3467	0.995	0.999	0.022	0.046	0.979	100
3.02-3.8	4.1	0.032	3463	0.997	0.999	0.018	0.037	0.681	99.9
3.8-50	4.1	0.028	3458	0.997	0.999	0.016	0.032	0.509	97.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.4→37.73 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1625	3435	2.88 %
R_work	0.1334	-	-
obs	0.1343	119219	87.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→37.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3138	0	54	526	3718

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3405
X-RAY DIFFRACTION	f_angle_d	1.07	4647
X-RAY DIFFRACTION	f_dihedral_angle_d	15.133	1338
X-RAY DIFFRACTION	f_chiral_restr	0.086	510
X-RAY DIFFRACTION	f_plane_restr	0.011	641

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 (%)
1.4-1.42	0.1907	55	0.1721	1880	X-RAY DIFFRACTION	35
1.42-1.44	0.175	66	0.1615	2182	X-RAY DIFFRACTION	41
1.44-1.46	0.1541	70	0.147	2476	X-RAY DIFFRACTION	47
1.46-1.48	0.1642	90	0.1429	2852	X-RAY DIFFRACTION	54
1.48-1.51	0.1795	104	0.1386	3468	X-RAY DIFFRACTION	65
1.51-1.53	0.1819	114	0.1317	4116	X-RAY DIFFRACTION	78
1.53-1.56	0.1569	141	0.1252	4770	X-RAY DIFFRACTION	89
1.56-1.59	0.1564	139	0.1242	4968	X-RAY DIFFRACTION	94
1.59-1.62	0.1555	169	0.1269	5129	X-RAY DIFFRACTION	97
1.62-1.66	0.1512	136	0.1319	5208	X-RAY DIFFRACTION	99
1.66-1.7	0.1845	132	0.1321	5228	X-RAY DIFFRACTION	100
1.7-1.74	0.1766	146	0.1335	5303	X-RAY DIFFRACTION	100
1.74-1.79	0.1633	167	0.1289	5287	X-RAY DIFFRACTION	100
1.79-1.84	0.1821	165	0.1298	5216	X-RAY DIFFRACTION	100
1.84-1.9	0.1713	156	0.1352	5281	X-RAY DIFFRACTION	99
1.9-1.97	0.1907	167	0.137	5245	X-RAY DIFFRACTION	99
1.97-2.05	0.1144	164	0.1316	5240	X-RAY DIFFRACTION	100
2.05-2.14	0.1716	153	0.1266	5267	X-RAY DIFFRACTION	100
2.14-2.25	0.1436	170	0.1342	5272	X-RAY DIFFRACTION	99
2.25-2.39	0.1601	160	0.1312	5240	X-RAY DIFFRACTION	100
2.39-2.58	0.167	149	0.1406	5296	X-RAY DIFFRACTION	100
2.58-2.84	0.1611	166	0.1499	5252	X-RAY DIFFRACTION	100
2.84-3.25	0.1864	150	0.139	5298	X-RAY DIFFRACTION	100
3.25-4.09	0.1433	150	0.123	5215	X-RAY DIFFRACTION	99
4.09-37.73	0.17	156	0.1307	5095	X-RAY DIFFRACTION	96

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	1.2703	1.4527	0.0741	8.2655	-1.0041	5.9855	0.1609	0.3788	0.3001	0.0415	0.1125	0.3855	-0.1575	-0.5433	-0.2718	0.1839	0.0524	-0.0133	0.1637	0.0381	0.1372	5.3204	28.7055	-4.977
2	0.7737	0.1315	-0.3135	1.0068	0.0116	0.7733	0.0214	-0.1541	-0.0641	0.1076	-0.0015	-0.1293	0.0588	0.1502	-0.0221	0.095	0.0066	-0.0074	0.1258	-0.0053	0.1155	21.7389	18.6075	19.6284
3	2.4574	-0.4524	0.7862	2.5665	-0.9553	4.1616	0.0861	0.0674	0.317	-0.0873	-0.0283	-0.1584	-0.3055	0.1529	0.0267	0.101	-0.0199	0.0384	0.0923	-0.0045	0.1714	25.462	32.1926	9.6236
4	0.8752	0.1346	-0.2315	0.9019	0.0644	0.728	0.0074	-0.0844	0.0126	0.098	-0.0091	0.0114	-0.0195	-0.0011	-0.0087	0.0846	0.0096	-0.0048	0.0857	-0.0021	0.0777	7.1071	20.9127	21.7257
5	1.709	2.0382	0.8961	3.0245	0.5355	1.5432	0.0405	0.0255	-0.5883	0.1233	0.0209	-0.2831	0.4371	0.2218	-0.0036	0.2204	0.0578	0.0208	0.1759	0.0066	0.2963	15.0263	-4.5115	16.1965
6	2.3153	-0.887	0.1347	2.0167	-0.8866	1.1989	-0.0063	0.0376	-0.2834	-0.0273	0.0178	0.1782	0.1358	-0.1029	0.0588	0.1071	-0.0166	-0	0.1076	-0.015	0.1254	-2.545	5.2881	13.3532
7	0.7968	0.0381	-0.0295	0.5681	0.0774	0.824	0.0292	0.0684	-0.0135	-0.0297	-0.0074	-0.0642	0.0224	0.0819	-0.0265	0.0904	0.0058	0.0027	0.084	-0.0006	0.0902	19.1433	21.4467	4.6572
8	0.9452	-0.0191	-0.5802	1.1356	0.1118	1.0888	-0.0132	0.1043	-0.1191	-0.0875	-0.0802	-0.0077	0.0889	-0.1023	0.0272	0.1165	0.001	-0.0071	0.129	-0.0155	0.0947	8.9231	10.4756	-6.5919
9	2.0061	-2.6941	-2.7721	2.0032	6.1509	5.851	-0.0182	0.6388	0.182	-0.396	0.0178	0.2898	-0.1961	-0.296	0.001	0.1969	0.032	-0.06	0.3586	-0.0242	0.1632	-1.2728	13.7983	-11.169
10	1.3498	-0.4306	0.4388	0.8415	-0.3827	1.4238	-0.0256	0.0359	-0.2689	-0.0506	0.0321	0.1855	0.1593	-0.0855	0.0361	0.154	-0.0136	-0.0064	0.1521	-0.0266	0.1752	1.4574	3.8967	2.8493
11	2.0024	-0.7498	1.853	4.1613	-0.3227	4.9884	-0.0755	0.0688	-0.188	0.187	0.0003	-0.3222	0.0997	0.313	0.0784	0.2232	0.104	-0.0019	0.3419	-0.0115	0.2347	18.2041	-1.4628	9.6213

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 19:28)
2	X-RAY DIFFRACTION	2	(chain A and resid 29:67)
3	X-RAY DIFFRACTION	3	(chain A and resid 68:88)
4	X-RAY DIFFRACTION	4	(chain A and resid 89:229)
5	X-RAY DIFFRACTION	5	(chain A and resid 230:246)
6	X-RAY DIFFRACTION	6	(chain A and resid 247:278)
7	X-RAY DIFFRACTION	7	(chain A and resid 279:334)
8	X-RAY DIFFRACTION	8	(chain A and resid 335:388)
9	X-RAY DIFFRACTION	9	(chain A and resid 389:393)
10	X-RAY DIFFRACTION	10	(chain A and resid 394:410)
11	X-RAY DIFFRACTION	11	(chain A and resid 411:418)

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