9u8o

Crystal structure of cupin-domain containing protein (AzcA) forming triazine (6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid) moiety from Streptomyces mobaraensis in complex with manganese and 2,5,6-triaminopyrimidin-4(3H)-one.

Method: X-RAY DIFFRACTION

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

Cupin type-2 domain-containing protein

Streptomyces mobaraensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2,5,6-tris(azanyl)-5~{H}-pyrimidin-4-one × 1 IMIDAZOLE × 1 MANGANESE (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (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	A0A7X1IDL3_9ACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–100； UniProt 2–96 Author chain B； PDBConstruct 6–100； UniProt 2–96

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	9u8o
Deposition date deposition_date	2025-03-26
Last revision last_revision	2026-04-01
Structure title title	Crystal structure of cupin-domain containing protein (AzcA) forming triazine (6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid) moiety from Streptomyces mobaraensis in complex with manganese and 2,5,6-triaminopyrimidin-4(3H)-one.
Keywords keywords	cupin-domain containing protein, AzcA, 5-azacytidine biosynthesis, 2, 5, 6-triaminopyrimidin-4(3H)-one, 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.

9u8o__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9u8o__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9u8o__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	13.85 Å
Rg (electron density)	12.61 Å
Total Rg	13.83 Å
Atom count	732
Residues	93
Excluded volume	12797 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9u8o__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9u8o__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 (5)

Entity 1 Entity 1 polymer

Description description	Cupin type-2 domain-containing protein
Molecular weight formula_weight	11212.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1627

MHEHIEQVGTKLVYSDDRVRVWVLELEAGEQTIVHQHPCDYVYVVTESGRAETVNHDGTSYVGDDKVGDAVYHEAGQPHLLRNIGDTHYSNIIVELLATG

Source Source

Source organism organism	Streptomyces mobaraensis
NCBI taxonomy ID ncbi_taxonomy_id	35621
Host organism host_organism	Escherichia coli M15

Entity 2 Entity 2 non-polymer

Description description	2,5,6-tris(azanyl)-5~{H}-pyrimidin-4-one
Molecular weight formula_weight	141.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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Unit-cell length a length_a	42.086 Å
Unit-cell length b length_b	42.086 Å
Unit-cell length c length_c	198.614 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	1.710 Å
Low-resolution limit resolution_low	41.170 Å
R factor r_factor	0.1880
R_work r_work	0.1840
R_free r_free	0.2255

Crystal structure of cupin-domain containing protein (AzcA) forming triazine (6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid) moiety from Streptomyces mobaraensis in complex with manganese and 2,5,6-triaminopyrimidin-4(3H)-one.

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

Cupin type-2 domain-containing protein

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

9u8o__assembly_2__model_1

9u8o__assembly_2__model_1 | I(q)

9u8o__assembly_2__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 (5)

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 water

7. Citations (1)

Crystal structure of cupin-domain containing protein (AzcA) forming triazine (6-amino-4-oxo-4,5-dihydro-1,3,5-triazine-2-carboxylic acid) moiety from Streptomyces mobaraensis in complex with manganese and 2,5,6-triaminopyrimidin-4(3H)-one.

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

Cupin type-2 domain-containing protein

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

9u8o__assembly_2__model_1

9u8o__assembly_2__model_1 | I(q)

9u8o__assembly_2__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 (5)

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 water

7. Citations (1)