2vxa

H. halophila dodecin in complex with riboflavin

Method: X-RAY DIFFRACTION

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

DODECIN

HALORHODOSPIRA HALOPHILA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	RIBOFLAVIN × 12 CHLORIDE ION × 24	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1WUH0_HALHL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–70； UniProt 1–70 Author chain B； PDBConstruct 1–70； UniProt 1–70 Author chain C； PDBConstruct 1–70； UniProt 1–70 Author chain D； PDBConstruct 1–70； UniProt 1–70 Author chain E； PDBConstruct 1–70； UniProt 1–70 Author chain F； PDBConstruct 1–70； UniProt 1–70 Author chain G； PDBConstruct 1–70； UniProt 1–70 Author chain H； PDBConstruct 1–70； UniProt 1–70 Author chain I； PDBConstruct 1–70； UniProt 1–70 Author chain J； PDBConstruct 1–70； UniProt 1–70 Author chain K； PDBConstruct 1–70； UniProt 1–70 Author chain L； PDBConstruct 1–70； UniProt 1–70

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	2vxa
Deposition date deposition_date	2008-07-01
Structure title title	H. halophila dodecin in complex with riboflavin
Keywords keywords	FLAVOPROTEIN, DODECIN, FLAVIN, RIBOFLAVIN, LUMICHROME, ARCHAEA; 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.

2vxa__assembly_1__model_1

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

Download this curve (.dat)

2vxa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vxa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.33 Å
Rg (electron density)	25.72 Å
Total Rg	26.53 Å
Atom count	6615
Residues	804
Excluded volume	115790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vxa__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 (3)

Entity 1 Entity 1 polymer

Description description	DODECIN
Molecular weight formula_weight	7995.9 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	6615

MSDHVYKIVELTGSSPNGIEEAVNNAIARAGETLRHLRWFEVVDTRGHIEGGRVNHWQVTVKVGFTLEGGLE

Source Source

Source organism organism	HALORHODOSPIRA HALOPHILA
NCBI taxonomy ID ncbi_taxonomy_id	1053
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	RIBOFLAVIN
Molecular weight formula_weight	376.4 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	24

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2vxaa_
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	d2vxab_
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	d2vxac_
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	d2vxad_
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	d2vxae_
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	d2vxaf_
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	d2vxag_
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	d2vxah_
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	d2vxai_
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	d2vxaj_
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	d2vxak_
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	d2vxal_
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 (12 domains)

Domain ID domain_id	2vxaA00
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	2vxaB00
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	2vxaC00
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	2vxaD00
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	2vxaE00
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	2vxaF00
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	2vxaG00
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	2vxaH00
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	2vxaI00
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	2vxaJ00
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	2vxaK00
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	2vxaL00
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	85.760 Å
Unit-cell length b length_b	100.510 Å
Unit-cell length c length_c	100.470 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	2.600 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2530
R_work r_work	0.2510
R_free r_free	0.2880

H. halophila dodecin in complex with riboflavin

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

2vxa__assembly_1__model_1

2vxa__assembly_1__model_1 | I(q)

2vxa__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

H. halophila dodecin in complex with riboflavin

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

2vxa__assembly_1__model_1

2vxa__assembly_1__model_1 | I(q)

2vxa__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)