SAXSdb — 2yj0

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

DODECIN

MYCOBACTERIUM TUBERCULOSIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE × 12 COENZYME A × 12 FLAVIN MONONUCLEOTIDE × 12 CHLORIDE ION × 6 SULFATE ION × 4 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8VK10_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 2–70 Author chain B； PDBConstruct 1–69； UniProt 2–70 Author chain C； PDBConstruct 1–69； UniProt 2–70 Author chain D； PDBConstruct 1–69； UniProt 2–70 Author chain E； PDBConstruct 1–69； UniProt 2–70 Author chain F； PDBConstruct 1–69； UniProt 2–70

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	2yj0
Deposition date deposition_date	2011-05-17
Structure title title	X-ray structure of chemically engineered Mycobacterium tuberculosis Dodecin
Keywords keywords	FLAVOPROTEIN, FLAVIN BINDING PROTEIN, PROTEIN-ENGINEERING, PUTATIVE STORAGE PROTEIN, DODECIN HYBRID; FLAVOPROTEIN
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.

2yj0__assembly_1__model_1

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

Download this curve (.dat)

2yj0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yj0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.07 Å
Rg (electron density)	26.22 Å
Total Rg	27.09 Å
Atom count	7106
Residues	814
Excluded volume	123810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yj0__assembly_1__model_1`	dodecameric （12）	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	DODECIN
Molecular weight formula_weight	7508.5 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4001

SNHTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVCMKVGFRLEDS

Source Source

Source organism organism	MYCOBACTERIUM TUBERCULOSIS
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE
Molecular weight formula_weight	461.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2yj0a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d2yj0b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d2yj0c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d2yj0d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d2yj0e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

Domain ID domain_id	d2yj0f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.2 — Dodecin-like
Family Family family	d.230.2.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	2yj0A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	2yj0B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	2yj0C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	2yj0D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	2yj0E00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

Domain ID domain_id	2yj0F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1660 — Dodecin subunit-like
Homologous superfamily homologous superfamily	10 — Flavin-binding protein dodecin

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Unit-cell length a length_a	94.000 Å
Unit-cell length b length_b	103.800 Å
Unit-cell length c length_c	82.500 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2204
R_work r_work	0.2169
R_free r_free	0.2749

X-ray structure of chemically engineered Mycobacterium tuberculosis Dodecin

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

DODECIN

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

2yj0__assembly_1__model_1

2yj0__assembly_1__model_1 | I(q)

2yj0__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

X-ray structure of chemically engineered Mycobacterium tuberculosis Dodecin

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

DODECIN

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

2yj0__assembly_1__model_1

2yj0__assembly_1__model_1 | I(q)

2yj0__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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)