2v18

Crystal structure of the T. thermophilus dodecin

Method: X-RAY DIFFRACTION

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

DODECIN

THERMUS THERMOPHILUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	FLAVIN MONONUCLEOTIDE × 12 COENZYME A × 9 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SIE3_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–68； UniProt 2–69 Author chain B； PDBConstruct 1–68； UniProt 2–69 Author chain C； PDBConstruct 1–68； UniProt 2–69 Author chain D； PDBConstruct 1–68； UniProt 2–69 Author chain E； PDBConstruct 1–68； UniProt 2–69 Author chain F； PDBConstruct 1–68； UniProt 2–69 Author chain G； PDBConstruct 1–68； UniProt 2–69 Author chain H； PDBConstruct 1–68； UniProt 2–69 Author chain I； PDBConstruct 1–68； UniProt 2–69 Author chain J； PDBConstruct 1–68； UniProt 2–69 Author chain K； PDBConstruct 1–68； UniProt 2–69 Author chain L； PDBConstruct 1–68； UniProt 2–69

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	2v18
Deposition date deposition_date	2007-05-22
Structure title title	Crystal structure of the T. thermophilus dodecin
Keywords keywords	;FLAVOPROTEIN, HYPOTHETICAL PROTEIN, FLAVIN BINDING PROTEIN, DODECINS, COENZYME A, FLAVIN DIMER, FLAVOPROTEIN PUTATIVE STORAGE PROTEIN ;; 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.

2v18__assembly_1__model_1

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

Download this curve (.dat)

2v18__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v18__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.53 Å
Rg (electron density)	26.50 Å
Total Rg	27.59 Å
Atom count	7176
Residues	816
Excluded volume	126700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v18__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 (4)

Entity 1 Entity 1 polymer

Description description	DODECIN
Molecular weight formula_weight	7628.7 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	7201

GKVYKKVELVGTSEEGLEAAIQAALARARKTLRHLDWFEVKEIRGTIGEAGVKEYQVVLEVGFRLEET

Source Source

Source organism organism	THERMUS THERMOPHILUS
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	12

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	9

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2v18a_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18b_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18c_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18d_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18e_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18f_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18g_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18h_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18i_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18j_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18k_
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.230.2.1 — Dodecin-like

Domain ID domain_id	d2v18l_
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.230.2.1 — Dodecin-like

CATH v4.4 (12 domains)

Domain ID domain_id	2v18A00
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	2v18B00
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	2v18C00
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	2v18D00
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	2v18E00
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	2v18F00
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	2v18G00
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	2v18H00
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	2v18I00
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	2v18J00
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	2v18K00
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	2v18L00
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	67.481 Å
Unit-cell length b length_b	98.038 Å
Unit-cell length c length_c	137.595 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.590 Å
Low-resolution limit resolution_low	24.760 Å
R factor r_factor	0.2200
R_work r_work	0.2190
R_free r_free	0.2440

Crystal structure of the T. thermophilus 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

2v18__assembly_1__model_1

2v18__assembly_1__model_1 | I(q)

2v18__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the T. thermophilus 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

2v18__assembly_1__model_1

2v18__assembly_1__model_1 | I(q)

2v18__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)