SAXSdb — 8uav

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

Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2

Brucella abortus biovar 1 (strain 9-941)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 8–158 Chain B； UniProt 8–158 Chain C； UniProt 8–158 Chain D； UniProt 8–158 Chain E； UniProt 8–158 Chain F； UniProt 8–158 Chain G； UniProt 8–158 Chain H； UniProt 8–158 Chain I； UniProt 8–158 Chain J； UniProt 8–158	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.37 Å

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 8UAV	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 method 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 oligomeric state Different ligand/ion Different experimental method 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
1XN1 Crystal Structure Of Lumazine Synthase From Brucella Abortus (Orthorhombic Form At 3.05 Angstroms) Deposited 2004-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 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） Chain F 1–158（158 aa） Chain G 1–158（158 aa） Chain H 1–158（158 aa） Chain I 1–158（158 aa） Chain J 1–158（158 aa）	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
8UAW Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin II subunit B (Stx2B) Deposited 2023-09-22	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 83–233； UniProt 8–158 Author chain B； PDBConstruct 83–233； UniProt 8–158 Author chain C； PDBConstruct 83–233； UniProt 8–158 Author chain D； PDBConstruct 83–233； UniProt 8–158 Author chain E； PDBConstruct 83–233； UniProt 8–158 Author chain F； PDBConstruct 83–233； UniProt 8–158 Author chain G； PDBConstruct 83–233； UniProt 8–158 Author chain H； PDBConstruct 83–233； UniProt 8–158 Author chain I； PDBConstruct 83–233； UniProt 8–158 Author chain J； PDBConstruct 83–233； UniProt 8–158

Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2

Brucella abortus biovar 1 (strain 9-941)

UniProt Q7DH26

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Homooligomer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 21–89 Chain B； UniProt 21–89 Chain C； UniProt 21–89 Chain D； UniProt 21–89 Chain E； UniProt 21–89 Chain F； UniProt 21–89 Chain G； UniProt 21–89 Chain H； UniProt 21–89 Chain I； UniProt 21–89 Chain J； UniProt 21–89	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.37 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q7DH26_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–71； UniProt 21–89 Author chain B； PDBConstruct 3–71； UniProt 21–89 Author chain C； PDBConstruct 3–71； UniProt 21–89 Author chain D； PDBConstruct 3–71； UniProt 21–89 Author chain E； PDBConstruct 3–71； UniProt 21–89 Author chain F； PDBConstruct 3–71； UniProt 21–89 Author chain G； PDBConstruct 3–71； UniProt 21–89 Author chain H； PDBConstruct 3–71； UniProt 21–89 Author chain I； PDBConstruct 3–71； UniProt 21–89 Author chain J； PDBConstruct 3–71； UniProt 21–89

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	8uav
Deposition date deposition_date	2023-09-22
Structure title title	Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B)
Keywords keywords	CHIMERA, SHIGA, TOXIN, IMMUNOGEN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	47.88 Å
Radius of gyration Rg (electron density) rg_electron	47.67 Å
Forward intensity I(0) i0	921420000.00
Molecular weight molecular_weight	251240.0 kDa
Excluded volume excluded_volume	314550 Å³
Envelope volume envelope_volume	442340 Å³
Hydration-shell volume shell_volume	80142 Å³
Envelope diameter envelope_diameter	158.2 Å
Shell Rg shell_rg	49.46 Å
Envelope Rg envelope_rg	47.16 Å
Shape Rg shape_rg	47.59 Å
Total Rg total_rg	48.04 Å
Total atoms total_atoms	17740
Residues n_residues	2310
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

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

Maximum dimension Dmax dmax	151.4 Å
Rg (real space) rg_real	48.37 Å
Rg uncertainty (real space) rg_real_error	1.43 Å
I(0) (real space) i0_real	9.2140e+08
I(0) uncertainty (real space) i0_real_error	1.6970e+07
Rg (reciprocal space) rg_reciprocal	47.88 Å
I(0) (reciprocal space) i0_reciprocal	920800000.0000
Solution quality estimate total_estimate	0.7905
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	50.5 Å
Skewness Skewness skewness	0.642
Kurtosis Kurtosis kurtosis	-0.071
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	407600000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.724; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.102

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.37 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	88636

Description description	Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2
Molecular weight formula_weight	25390.8 kDa
EC 编号 ec_number	2.5.1.78
Source method src_method	man
Copy count entity_count	10

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	17740

Cryo-EM Structure of Brucella Abortus Lumazine Synthase (BLS) Engineered with Shiga Toxin I subunit B (Stx1B)

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

Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2

State in the Current Structure

Other States of the Same Protein in the Database

Shiga toxin subunit B,6,7-dimethyl-8-ribityllumazine synthase 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Brucella abortus biovar 1 (strain 9-941)
NCBI Class编号 ncbi_taxonomy_id	262698
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/ua/8uav/8uav.fit
pddf	/app/data/pr_computation/ua/8uav/8uav.pr.out
profile	/app/data/saxs_computation/ua/8uav/8uav.dat