SAXSdb — 2vkg

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

DODECIN

HALOBACTERIUM SALINARUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	MAGNESIUM ION × 24 SODIUM ION × 12 [4-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)butyl]carbamic acid × 12 CHLORIDE ION × 12 SULFATE ION × 12 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9HPW4_HALSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–48； UniProt 11–58 Author chain A； PDBConstruct 49–62； UniProt 61–74

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	2vkg
Deposition date deposition_date	2007-12-19
Structure title title	COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS
Keywords keywords	BIOTECHNOLOGICAL APPLICATION OF DODECIN BINDING PROPERTIES, FLAVIN-DNA LIGAND HYBRID, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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.

2vkg__assembly_1__model_1

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

Download this curve (.dat)

2vkg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vkg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.81 Å
Rg (electron density)	25.22 Å
Total Rg	26.13 Å
Atom count	6064
Residues	744
Excluded volume	106570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vkg__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	6722.3 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	605

VFKKVLLTGTSEESFTAAADDAIDRAEDTLDNVVWAEVVDQGVAIGAVRTYQTEVQVAFELD

Source Source

Source organism organism	HALOBACTERIUM SALINARUM
NCBI taxonomy ID ncbi_taxonomy_id	478009
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	[4-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)butyl]carbamic acid
Molecular weight formula_weight	357.4 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

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	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	86

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2vkga_
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 (1 domains)

Domain ID domain_id	2vkgA00
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	142.030 Å
Unit-cell length b length_b	142.030 Å
Unit-cell length c length_c	142.030 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	96

Space group space_group	F 41 3 2
Space-group number int_tables_number	210
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.750 Å
R factor r_factor	0.1930
R_work r_work	0.1920
R_free r_free	0.2130

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

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

2vkg__assembly_1__model_1

2vkg__assembly_1__model_1 | I(q)

2vkg__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

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

2vkg__assembly_1__model_1

2vkg__assembly_1__model_1 | I(q)

2vkg__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)