1xn1

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

Method: X-RAY DIFFRACTION D_max: 102.3 Å Quality: GOOD

▼

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

6,7-dimethyl-8-ribityllumazine synthase

Brucella abortus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–158 Chain B； UniProt 1–158 Chain C； UniProt 1–158 Chain D； UniProt 1–158 Chain E； UniProt 1–158 Chain F； UniProt 1–158 Chain G； UniProt 1–158 Chain H； UniProt 1–158 Chain I； UniProt 1–158 Chain J； UniProt 1–158	Not recorded	PO4 PHOSPHATE ION × 24 NA SODIUM ION × 7 SO4 SULFATE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；1.3M AMMONIUM SULFATE, 0.1M NA MES, PH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.05 Å R-free 0.256

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1XN1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DI0 CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS Deposited 1999-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa）	Not recorded	PO4 PHOSPHATE ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；1.2 M ammonium sulfate, 0.1M phoshate buffer, pH 5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.230
1DI0 CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS Deposited 1999-11-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–158（158 aa） Chain B 1–158（158 aa） Chain C 1–158（158 aa） Chain D 1–158（158 aa） Chain E 1–158（158 aa）	Not recorded	PO4 PHOSPHATE ION × 26	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；1.2 M ammonium sulfate, 0.1M phoshate buffer, pH 5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.230
8UAV Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B) Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 8–158（151 aa） Chain B 8–158（151 aa） Chain C 8–158（151 aa） Chain D 8–158（151 aa） Chain E 8–158（151 aa） Chain F 8–158（151 aa） Chain G 8–158（151 aa） Chain H 8–158（151 aa） Chain I 8–158（151 aa） Chain J 8–158（151 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.37 Å
8UAW Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin II subunit B (Stx2B) Deposited 2023-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 8–158（151 aa） Chain B 8–158（151 aa） Chain C 8–158（151 aa） Chain D 8–158（151 aa） Chain E 8–158（151 aa） Chain F 8–158（151 aa） Chain G 8–158（151 aa） Chain H 8–158（151 aa） Chain I 8–158（151 aa） Chain J 8–158（151 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

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

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.50 Å
Radius of gyration Rg (electron density) rg_electron	32.76 Å
Forward intensity I(0) i0	420364000.00
Molecular weight molecular_weight	164040.0 kDa
Excluded volume excluded_volume	204160 Å³
Envelope volume envelope_volume	239360 Å³
Hydration-shell volume shell_volume	57973 Å³
Envelope diameter envelope_diameter	107.0 Å
Shell Rg shell_rg	41.96 Å
Envelope Rg envelope_rg	32.51 Å
Shape Rg shape_rg	32.71 Å
Total Rg total_rg	33.55 Å
Total atoms total_atoms	11562
Residues n_residues	1444
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	102.3 Å
Rg (real space) rg_real	33.31 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	4.2040e+08
I(0) uncertainty (real space) i0_real_error	6.0160e+06
Rg (reciprocal space) rg_reciprocal	33.43 Å
I(0) (reciprocal space) i0_reciprocal	420400000.0000
Solution quality estimate total_estimate	0.9000
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.5 Å
Skewness Skewness skewness	0.127
Kurtosis Kurtosis kurtosis	-0.495
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	210500000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.946

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. 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

来源 Source

来源生物 organism	Brucella abortus
NCBI Class编号 ncbi_taxonomy_id	235
宿主生物 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

▼

7. 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

▶

8. Citations (1)

▶

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

fit	/app/data/saxs_computation/xn/1xn1/1xn1.fit
pddf	/app/data/pr_computation/xn/1xn1/1xn1.pr.out
profile	/app/data/saxs_computation/xn/1xn1/1xn1.dat