1xn1

Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)

Method: X-RAY DIFFRACTION

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

6,7-dimethyl-8-ribityllumazine synthase

Brucella abortus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	PHOSPHATE ION × 24 SODIUM ION × 7 SULFATE ION × 15 water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RISB2_BRUAB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158 Author chain B； PDBConstruct 1–158； UniProt 1–158 Author chain C； PDBConstruct 1–158； UniProt 1–158 Author chain D； PDBConstruct 1–158； UniProt 1–158 Author chain E； PDBConstruct 1–158； UniProt 1–158 Author chain F； PDBConstruct 1–158； UniProt 1–158 Author chain G； PDBConstruct 1–158； UniProt 1–158 Author chain H； PDBConstruct 1–158； UniProt 1–158 Author chain I； PDBConstruct 1–158； UniProt 1–158 Author chain J； PDBConstruct 1–158； UniProt 1–158

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	1xn1
Deposition date deposition_date	2004-10-04
Structure title title	Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)
Keywords keywords	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.

1xn1__assembly_1__model_1

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

Download this curve (.dat)

1xn1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xn1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.50 Å
Rg (electron density)	32.76 Å
Total Rg	33.55 Å
Atom count	11562
Residues	1474
Excluded volume	204160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xn1__assembly_1__model_1`	decameric （10）	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 (5)

Entity 1 Entity 1 polymer

Description description	6,7-dimethyl-8-ribityllumazine synthase
Molecular weight formula_weight	17381.9 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	11578

MNQSCPNKTSFKIAFIQARWHADIVDEARKSFVAELAAKTGGSVEVEIFDVPGAYEIPLHAKTLARTGRYAAIVGAAFVIDGGIYRHDFVATAVINGMMQVQLETEVPVLSVVLTPHHFHESKEHHDFFHAHFKVKGVEAAHAALQIVSERSRIAALV

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	24

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	7

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1xn1a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

Domain ID domain_id	d1xn1j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.16 — Lumazine synthase
Superfamily Superfamily superfamily	c.16.1 — Lumazine synthase
Family Family family	c.16.1.1 — Lumazine synthase

CATH v4.4 (10 domains)

Domain ID domain_id	1xn1A00
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	1xn1B00
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	1xn1C00
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	1xn1D00
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	1xn1E00
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	1xn1F00
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	1xn1G00
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	1xn1H00
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	1xn1I00
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	1xn1J00
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	116.554 Å
Unit-cell length b length_b	120.238 Å
Unit-cell length c length_c	159.372 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	40

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	56.000 Å
R factor r_factor	0.2020
R_work r_work	0.1990
R_free r_free	0.2560

Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)

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

6,7-dimethyl-8-ribityllumazine synthase

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

1xn1__assembly_1__model_1

1xn1__assembly_1__model_1 | I(q)

1xn1__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms)

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

6,7-dimethyl-8-ribityllumazine synthase

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

1xn1__assembly_1__model_1

1xn1__assembly_1__model_1 | I(q)

1xn1__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)