PDB-9p3c: Structure of radical S-adenosylmethionine methyltransferase, NocN...

ID or keywords:

Entry

Database: PDB / ID: 9p3c

Title

Structure of radical S-adenosylmethionine methyltransferase, NocN, from Nocardia with SAH and side-ring closed product analog bound

Components

radical S-adenosylmethionine methyltransferase NocN

Keywords

OXIDOREDUCTASE / radical S-adenosylmethionine / nosiheptide / nocathiacin

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 /

MOLECULAR REPLACEMENT / Resolution: 1.78 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 13, 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	9p3c.cif.gz	424.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9p3c.ent.gz		Display	PDB format
PDBx/mmJSON format	9p3c.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/p3/9p3c ftp://data.pdbj.org/pub/pdb/validation_reports/p3/9p3c	HTTPS FTP

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Related structure data

Related structure data	9p2uC 9p3bC 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

B: radical S-adenosylmethionine methyltransferase NocN

A: radical S-adenosylmethionine methyltransferase NocN

hetero molecules

99.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: radical S-adenosylmethionine methyltransferase NocN

hetero molecules

defined by author&software
Evidence: gel filtration
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: radical S-adenosylmethionine methyltransferase NocN

hetero molecules

defined by author&software
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.926, 88.035, 146.897
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
d_1	ens_1	(chain "A" and (resid 20 through 180 or resid 182...
d_2	ens_1	(chain "B" and (resid 20 through 180 or resid 182...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	ASN	ASN	ARG	ARG	A	B	20 - 180	20 - 180
d_1	2	VAL	VAL	ILE	ILE	A	B	182 - 197	182 - 197
d_1	3	SER	SER	THR	THR	A	B	199 - 235	199 - 235
d_1	4	GLU	GLU	LYS	LYS	A	B	245 - 246	245 - 246
d_1	5	ALA	ALA	LEU	LEU	A	B	248 - 250	248 - 250
d_1	6	LYS	LYS	ALA	ALA	A	B	252 - 285	252 - 285
d_1	7	TYR	TYR	PHE	PHE	A	B	287 - 342	287 - 342
d_1	8	GLN	GLN	ALA	ALA	A	B	344 - 348	344 - 348
d_1	9	PHE	PHE	PRO	PRO	A	B	350 - 373	350 - 373
d_1	10	ILE	ILE	GLU	GLU	A	B	375 - 411	375 - 411
d_1	11	ALA	ALA	MET	MET	A	B	413 - 414	413 - 414
d_1	12	SF4	SF4	SF4	SF4	A	H	501
d_1	13	SAH	SAH	SAH	SAH	A	I	1101
d_1	14	SR4	SR4	SR4	SR4	A	K	1202
d_1	15	SR4	SR4	SR4	SR4	A	L	1203
d_2	1	ASN	ASN	ARG	ARG	B	A	20 - 180	20 - 180
d_2	2	VAL	VAL	ILE	ILE	B	A	182 - 197	182 - 197
d_2	3	SER	SER	LYS	LYS	B	A	199 - 246	199 - 246
d_2	4	ALA	ALA	LEU	LEU	B	A	248 - 250	248 - 250
d_2	5	LYS	LYS	ALA	ALA	B	A	252 - 285	252 - 285
d_2	6	TYR	TYR	PHE	PHE	B	A	287 - 342	287 - 342
d_2	7	GLN	GLN	ALA	ALA	B	A	344 - 348	344 - 348
d_2	8	PHE	PHE	PRO	PRO	B	A	350 - 373	350 - 373
d_2	9	ILE	ILE	GLU	GLU	B	A	375 - 411	375 - 411
d_2	10	ALA	ALA	MET	MET	B	A	413 - 414	413 - 414
d_2	11	SF4	SF4	SF4	SF4	B	C	501
d_2	12	SAH	SAH	SAH	SAH	B	D	801
d_2	13	SR4	SR4	SR4	SR4	B	F	902
d_2	14	SR4	SR4	SR4	SR4	B	G	903

NCS oper: (Code: givenMatrix: (-0.995527612704, -0.0527940485788, 0.0783425859874), (-0.0442980707236, 0.993327694944, 0.106478971578), (-0.0834413163529, 0.102532330964, -0.991223823277)Vector: -36. ...

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Protein , 1 types, 2 molecules BA

#1: Protein	radical S-adenosylmethionine methyltransferase NocN / Heme chaperone HemW Mass: 46377.559 Da / Num. of mol.: 2 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

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Non-polymers , 6 types, 778 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-A1CG2 / 2-[(6S,13S)-6-[(2-{(1S,2R)-1-[(N-{2-[(1S)-1-amino-2-hydroxyethyl]-1,3-thiazole-4-carbonyl}-L-threonyl)amino]-2-hydroxypropyl}-1,3-thiazole-4-carbonyl)amino]-18-methyl-3,11,16-trioxo-1,3,4,5,6,11,12,13,14,16-decahydro-10,7-(azeno)-17,19-epimino-2,15,8,12-benzodioxathiazacycloicosin-13-yl]-1,3-thiazole-4-carboxylic acid Mass: 1025.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄₂H₄₄N₁₀O₁₃S₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.09 Å³/Da / Density % sol: 41.11 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris pH 8.0, 100 mM CaCl2, 20% w/v PEG 6000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97856 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.78→50 Å / Num. obs: 117614 / % possible obs: 100 % / Redundancy: 8.2 % / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.025 / R_rim(I) all: 0.072 / Χ²: 0.905 / Net I/σ(I): 9.8

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
1.78-1.81	8.1	0.69	3741	0.857	0.961	0.256	0.736	0.763	100
1.81-1.84	8.1	0.588	3724	0.881	0.968	0.218	0.628	0.792	100
1.84-1.88	8.1	0.516	3723	0.912	0.977	0.191	0.551	0.812	100
1.88-1.92	8.2	0.437	3743	0.939	0.984	0.162	0.467	0.85	100
1.92-1.96	8.2	0.331	3720	0.958	0.989	0.123	0.353	0.903	100
1.96-2	8.2	0.263	3771	0.977	0.994	0.097	0.281	0.841	100
2-2.05	8.3	0.221	3730	0.984	0.996	0.081	0.236	0.859	100
2.05-2.11	8.2	0.189	3739	0.985	0.996	0.07	0.202	0.934	100
2.11-2.17	8.3	0.154	3766	0.988	0.997	0.057	0.165	0.916	100
2.17-2.24	8.3	0.145	3743	0.99	0.998	0.054	0.155	1.008	100
2.24-2.32	8.3	0.134	3801	0.991	0.998	0.049	0.143	1.147	100
2.32-2.42	8.3	0.108	3752	0.994	0.998	0.04	0.116	0.985	100
2.42-2.53	8.3	0.088	3790	0.996	0.999	0.032	0.094	0.916	100
2.53-2.66	8.3	0.072	3750	0.997	0.999	0.027	0.077	0.846	100
2.66-2.83	8.3	0.063	3801	0.997	0.999	0.023	0.068	0.894	100
2.83-3.04	8.3	0.058	3814	0.997	0.999	0.021	0.062	1.087	100
3.04-3.35	8.2	0.055	3810	0.998	0.999	0.02	0.058	1.357	100
3.35-3.83	8.2	0.038	3845	0.999	1	0.014	0.041	0.99	100
3.83-4.83	8.1	0.028	3878	0.999	1	0.01	0.03	0.628	100
4.83-50	7.6	0.028	4069	0.998	0.999	0.011	0.031	0.539	99.4

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
PHENIX	1.20.1_4487	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→29.5 Å / SU ML: 0.1591 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1935	3375	2.87 %
R_work	0.1612	114239	-
obs	0.1621	117614	81.11 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.78 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→29.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6125	0	399	766	7290

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0091	6787
X-RAY DIFFRACTION	f_angle_d	1.0124	9251
X-RAY DIFFRACTION	f_chiral_restr	0.0532	999
X-RAY DIFFRACTION	f_plane_restr	0.0076	1253
X-RAY DIFFRACTION	f_dihedral_angle_d	15.8555	2524

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 1.81920845278 Å

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 (%)
1.78-1.8	0.2981	85	0.2398	2543	X-RAY DIFFRACTION	43.32
1.8-1.83	0.2334	89	0.232	2830	X-RAY DIFFRACTION	48.64
1.83-1.86	0.2492	90	0.2232	2974	X-RAY DIFFRACTION	51.01
1.86-1.89	0.2419	96	0.217	3082	X-RAY DIFFRACTION	52.15
1.89-1.92	0.2481	98	0.2233	3125	X-RAY DIFFRACTION	53.74
1.92-1.95	0.2419	106	0.2027	3319	X-RAY DIFFRACTION	56.35
1.95-1.99	0.1977	103	0.1835	3618	X-RAY DIFFRACTION	61.23
1.99-2.03	0.2144	100	0.1711	3837	X-RAY DIFFRACTION	65.59
2.03-2.08	0.2009	124	0.1723	4197	X-RAY DIFFRACTION	71.59
2.08-2.12	0.2566	129	0.1684	4611	X-RAY DIFFRACTION	78.1
2.12-2.18	0.2221	132	0.1726	4992	X-RAY DIFFRACTION	85.09
2.18-2.24	0.208	162	0.1722	5306	X-RAY DIFFRACTION	90.53
2.24-2.3	0.2412	151	0.1705	5565	X-RAY DIFFRACTION	93.97
2.3-2.38	0.2322	174	0.1733	5676	X-RAY DIFFRACTION	97.37
2.38-2.46	0.2328	179	0.174	5835	X-RAY DIFFRACTION	99.47
2.46-2.56	0.2053	162	0.1733	5852	X-RAY DIFFRACTION	99.87
2.56-2.68	0.1814	172	0.1685	5876	X-RAY DIFFRACTION	99.88
2.68-2.82	0.2683	157	0.1705	5894	X-RAY DIFFRACTION	99.93
2.82-2.99	0.2059	181	0.1612	5859	X-RAY DIFFRACTION	99.95
2.99-3.22	0.2	171	0.1644	5881	X-RAY DIFFRACTION	99.98
3.23-3.55	0.1574	196	0.1452	5839	X-RAY DIFFRACTION	99.95
3.55-4.06	0.1562	166	0.1349	5859	X-RAY DIFFRACTION	100
4.06-5.11	0.1369	182	0.121	5864	X-RAY DIFFRACTION	99.92
5.11-29.5	0.175	170	0.1641	5805	X-RAY DIFFRACTION	98.94

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	1.09959430872	-0.539956549717	0.0620298170657	1.75024543903	0.31758196517	1.50246471389	-0.0583992328803	0.0244933623068	-0.133177852747	-0.184234166738	-0.028048123004	0.661840983513	-0.0714689378922	-0.218054675284	0.0553813285662	0.0415021451915	0.0206079522845	-0.0175944093306	0.15524940785	-0.0141447866088	0.314266931843	-34.4460249163	-23.4273680175	50.3161271421
2	3.59177639747	-0.0219855659812	-0.0111275908128	2.25176042481	-0.020468814398	1.41850688477	-0.224658100582	-0.254787100516	0.229764028277	0.237343437231	0.113868259547	-0.0912357163342	-0.0866060943808	0.330219591723	0.0448796070331	0.141715823934	0.082650251141	-0.0111985591911	0.250339696895	-0.0408490447032	0.108105266194	-18.5589430968	-18.3225600563	66.3664224612
3	1.18786806847	-0.612445774136	-0.0606764782258	1.95882266455	0.220093281973	0.688537426784	-0.0806349528804	-0.122709432719	-0.0502325214112	0.0736938700184	0.0642252046097	0.000476328479002	0.147364353018	0.137322647754	0.0277013224107	0.100967361644	0.0452546555413	0.0132493044265	0.135808745365	0.00606124705081	0.0971795290562	-16.8006987192	-33.7735034849	52.3783724231
4	1.64587266314	0.201195145959	0.47234022542	3.75278467933	0.620518112734	2.45397334345	0.00390856881627	-0.0832400685507	0.183732074818	0.236378345697	0.103916078467	-0.214438024664	-0.382907997202	0.192301141792	-0.0905928852992	0.116392689366	-0.0542498243476	0.0226956219175	0.181232883951	-0.00977489853967	0.137694534231	-0.908329883642	-26.8672508799	29.5190860571
5	0.959570314195	0.481106577392	-0.147871204667	1.36972151534	0.135350580158	0.826815070245	-0.0713962608087	0.0242331539145	0.108730663697	-0.210923356501	0.196069362082	-0.249379321064	-0.346654559909	0.391497019349	0.0615151484699	0.244360050528	-0.181302248184	0.0650719875298	0.201167332785	-0.0473750745837	0.18803458634	3.60834404942	-20.5048950457	15.4075391916
6	5.45435720933	1.46954234142	1.79984441152	3.18078507132	-1.57598252557	4.68454621427	-0.343223489274	-0.288943149182	0.573840912344	-0.300654593281	0.186646419161	0.2881987448	-0.632678355324	-0.572037560732	0.0486704759325	0.357532699262	-0.0306783686932	-0.078516478572	0.185573066041	-0.00896135892349	0.193393291324	-17.4416304776	-18.579485003	5.66352763869
7	0.491767494145	0.0208233658647	0.483666632523	0.82699896879	0.231632071198	1.40104404612	0.0153178429689	0.0095954250891	0.0203047882821	-0.022175532197	0.0448278826796	0.0313238039104	-0.128045475558	-0.0198088534638	-0.0379231946901	0.0656994066868	-0.0197771022782	0.0145492308137	0.10920691607	0.00847452110953	0.115676041979	-12.7527504324	-34.7766261384	17.5791114397

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	(chain A and resid 20:191)	A	F	20 - 191	1 - 172
2	2	(chain A and resid 192:278)	A	F	192 - 278	173 - 259
3	3	(chain A and resid 279:1201)	A	F - I	279 - 1201	260 - 1
4	4	(chain B and resid 20:86)	B	A	20 - 86	1 - 67
5	5	(chain B and resid 87:225)	B	A	87 - 225	68 - 206
6	6	(chain B and resid 226:266)	B	A	226 - 266	207 - 238
7	7	(chain B and resid 267:901)	B	A - C	267 - 901	239 - 389

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Protein , 1 types, 2 molecules BA

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Non-polymers , 6 types, 778 molecules

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-Basic information

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-Related structure data

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-Protein , 1 types, 2 molecules BA

-Non-polymers , 6 types, 778 molecules

-Details

-Experimental details

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Protein , 1 types, 2 molecules BA

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Non-polymers , 6 types, 778 molecules

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