9p3c

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

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

radical S-adenosylmethionine methyltransferase NocN

Nocardia sp. ATCC 202099

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 1 S-ADENOSYL-L-HOMOCYSTEINE × 2 ;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 ; × 2 CALCIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	IRON/SULFUR CLUSTER × 1 S-ADENOSYL-L-HOMOCYSTEINE × 2 ;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 ; × 2 CALCIUM ION × 1 NICKEL (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E5DUI5_9NOCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 1–420 Author chain B； PDBConstruct 1–420； UniProt 1–420

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9p3c
Deposition date deposition_date	2025-06-13
Structure title title	Structure of radical S-adenosylmethionine methyltransferase, NocN, from Nocardia with SAH and side-ring closed product analog bound
Keywords keywords	radical S-adenosylmethionine, nosiheptide, nocathiacin, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9p3c__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9p3c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9p3c__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.23 Å
Rg (electron density)	20.14 Å
Total Rg	20.97 Å
Atom count	3217
Residues	386
Excluded volume	56391 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9p3c__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9p3c__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	radical S-adenosylmethionine methyltransferase NocN
Molecular weight formula_weight	46377.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	7374

MSTAVSLSSLVDVVPAPAPNLPSSTDEQHMLMLYVHVPFCHSKCTFCDWVQAIPTKDLLRKPEDSVRKNYIRALVTEIETRGAQLRAAGQVPYVVYWGGGTASSLDNAEAEAIWGALDSAFDLSTVAEATIECSPDTVDKAKLEFFRGLGFNRVSSGVQSFDDARLRRLGRRHTAGEADRIVHHAREAGFDEVSIDIMSGFPDQELDELRATVEKAVSLPLTHLSLYSFRPTPGTFMRRKLAGTEKRAYLRKQQALFTEARRMIIDAGLPEYASGYFGRVSPFAAMYFQLRADTAGFGSGAISLVDRQFLSHAKGKLHAYIQDPLAYDIDVPAGQDRVLVSFLQAGLAMFDGVLREEWRVSTGTDLDEVLTRPSIAPLADFLRGRGLIEDERGIRLDPRLAGLTLIELAFEMAMSQPESA

Source Source

Source organism organism	Nocardia sp. ATCC 202099
NCBI taxonomy ID ncbi_taxonomy_id	930400
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;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 ;
Molecular weight formula_weight	1025.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	765

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Unit-cell length a length_a	59.926 Å
Unit-cell length b length_b	88.035 Å
Unit-cell length c length_c	146.897 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.780 Å
Low-resolution limit resolution_low	29.500 Å
R factor r_factor	0.1621
R_work r_work	0.1612
R_free r_free	0.1935

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

radical S-adenosylmethionine methyltransferase NocN

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9p3c__assembly_1__model_1

9p3c__assembly_1__model_1 | I(q)

9p3c__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

radical S-adenosylmethionine methyltransferase NocN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9p3c__assembly_1__model_1

9p3c__assembly_1__model_1 | I(q)

9p3c__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)