SAXSdb — 2xsc

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

SHIGA-LIKE TOXIN 1 SUBUNIT B

OrganismNot specified

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 × 5 PDB declaration: pentameric（5） 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	Fragment：RESIDUES 21-89	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；12% PEG8000, 50 MM MOPS PH7.0	Resolution 2.05 Å R-free 0.192

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 2XSC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C48 MUTATED SHIGA-LIKE TOXIN B SUBUNIT (G62T) Deposited 1999-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain B 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain C 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain D 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain E 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN	Mutation：G62T Mutation：G62T Mutation：G62T Mutation：G62T Mutation：G62T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.60 Å R-free 0.240
1CZG STRUCTURE OF THE G62T MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT Deposited 1999-09-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain B 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain C 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain D 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain E 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN	Mutation：G62T Mutation：G62T Mutation：G62T Mutation：G62T Mutation：G62T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20% PEG4000, 10% propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.50 Å R-free 0.251
1CZW STRUCTURE OF THE W34A MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT Deposited 1999-09-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain B 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain C 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain D 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain E 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN	Mutation：W34A Mutation：W34A Mutation：W34A Mutation：W34A Mutation：W34A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG 4000 0.2 M MGCL2 5% DIOXANE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.50 Å R-free 0.214
1CZW STRUCTURE OF THE W34A MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT Deposited 1999-09-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain G 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain H 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain I 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN Chain J 21–89（69 aa） Fragment：SHIGA-LIKE TOXIN I BINDING DOMAIN	Mutation：W34A Mutation：W34A Mutation：W34A Mutation：W34A Mutation：W34A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG 4000 0.2 M MGCL2 5% DIOXANE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.50 Å R-free 0.214

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

View Construct and Data Evidence

UniProt name	STXB_BPH30
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 21–89 Author chain B； PDBConstruct 1–69； UniProt 21–89 Author chain C； PDBConstruct 1–69； UniProt 21–89 Author chain D； PDBConstruct 1–69； UniProt 21–89 Author chain E； PDBConstruct 1–69； 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	2xsc
Deposition date deposition_date	2010-09-27
Structure title title	Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli
Keywords keywords	TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.36 Å
Radius of gyration Rg (electron density) rg_electron	21.00 Å
Forward intensity I(0) i0	26246600.00
Molecular weight molecular_weight	38644.0 kDa
Excluded volume excluded_volume	47985 Å³
Envelope volume envelope_volume	55608 Å³
Hydration-shell volume shell_volume	22183 Å³
Envelope diameter envelope_diameter	66.1 Å
Shell Rg shell_rg	27.33 Å
Envelope Rg envelope_rg	20.83 Å
Shape Rg shape_rg	20.93 Å
Total Rg total_rg	21.97 Å
Total atoms total_atoms	2703
Residues n_residues	345
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	67.1 Å
Rg (real space) rg_real	22.25 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.6250e+07
I(0) uncertainty (real space) i0_real_error	3.1340e+05
Rg (reciprocal space) rg_reciprocal	22.28 Å
I(0) (reciprocal space) i0_reciprocal	26250000.0000
Solution quality estimate total_estimate	0.9114
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.121
Kurtosis Kurtosis kurtosis	-0.609
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8253000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2xsca_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d2xscb_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d2xscc_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d2xscd_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

Domain ID domain_id	d2xsce_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.1 — Bacterial AB5 toxins, B-subunits

CATH v4.4 (5 domains)

Domain ID domain_id	2xscA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2xscB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2xscC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2xscD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2xscE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

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8. Citations (1)

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Unit-cell length a length_a	59.600 Å
Unit-cell length b length_b	102.400 Å
Unit-cell length c length_c	56.100 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	20

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

Resolution resolution	2.052 Å
Low-resolution limit resolution_low	24.634 Å
R factor r_factor	0.1448
R_work r_work	0.1423
R_free r_free	0.1917

Description description	SHIGA-LIKE TOXIN 1 SUBUNIT B
Molecular weight formula_weight	7698.6 kDa
Source method src_method	nat
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	2922

Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli

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

SHIGA-LIKE TOXIN 1 SUBUNIT B

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

fit	/app/data/saxs_computation/xs/2xsc/2xsc.fit
pddf	/app/data/pr_computation/xs/2xsc/2xsc.pr.out
profile	/app/data/saxs_computation/xs/2xsc/2xsc.dat