SAXSdb — 2i0f

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

6,7-dimethyl-8-ribityllumazine synthase 1

Brucella abortus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	CALCIUM ION × 5 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RISB1_BRUAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–157； UniProt 1–157 Author chain B； PDBConstruct 1–157； UniProt 1–157 Author chain C； PDBConstruct 1–157； UniProt 1–157 Author chain D； PDBConstruct 1–157； UniProt 1–157 Author chain E； PDBConstruct 1–157； UniProt 1–157

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	2i0f
Deposition date deposition_date	2006-08-10
Structure title title	Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1)
Keywords keywords	lumazine synthase RibH1, TRANSFERASE; TRANSFERASE
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.

2i0f__assembly_1__model_1

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

Download this curve (.dat)

2i0f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2i0f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.77 Å
Rg (electron density)	25.45 Å
Total Rg	26.27 Å
Atom count	5484
Residues	733
Excluded volume	96891 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2i0f__assembly_1__model_1`	pentameric （5）	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	6,7-dimethyl-8-ribityllumazine synthase 1
Molecular weight formula_weight	16807.7 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	5665

MEFLMSKHEADAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVHARREDKDKGGFAARAALTMIGLRKKFGA

Source Source

Source organism organism	Brucella abortus
NCBI taxonomy ID ncbi_taxonomy_id	235
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	2i0fA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	2i0fB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	2i0fC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	2i0fD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

Domain ID domain_id	2i0fE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	960 — Lumazine/riboflavin synthase

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Unit-cell length a length_a	124.101 Å
Unit-cell length b length_b	68.521 Å
Unit-cell length c length_c	90.649 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.220 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2449
R_work r_work	0.2423
R_free r_free	0.2870

Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1)

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

6,7-dimethyl-8-ribityllumazine synthase 1

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

2i0f__assembly_1__model_1

2i0f__assembly_1__model_1 | I(q)

2i0f__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 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

Lumazine synthase RibH1 from Brucella abortus (Gene BruAb1_0785, Swiss-Prot entry Q57DY1)

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

6,7-dimethyl-8-ribityllumazine synthase 1

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

2i0f__assembly_1__model_1

2i0f__assembly_1__model_1 | I(q)

2i0f__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 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)