1bos

SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR

Method: X-RAY DIFFRACTION D_max: 147.6 Å Quality: GOOD

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

SHIGA-LIKE TOXIN I B SUBUNIT

Phage h30, Enterobacteria phage H-19B

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Homooligomer Protein × 5 其他Polymer 13 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：RECEPTOR-BINDING DOMAIN	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 8 alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose × 5 GAL beta-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.80 Å R-free 0.226
2	Other combination Homooligomer Protein × 5 其他Polymer 12 PDB declaration: pentameric（5） Consistent with protein copy count	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	Fragment：RECEPTOR-BINDING DOMAIN	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 9 alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose × 3 GAL beta-D-galactopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.80 Å R-free 0.226
3	Other combination Homooligomer Protein × 5 其他Polymer 12 PDB declaration: pentameric（5） Consistent with protein copy count	Chain K； UniProt 21–89 Chain L； UniProt 21–89 Chain M； UniProt 21–89 Chain N； UniProt 21–89 Chain O； UniProt 21–89	Fragment：RECEPTOR-BINDING DOMAIN	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 7 alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose × 5 GAL beta-D-galactopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.80 Å R-free 0.226
4	Other combination Homooligomer Protein × 5 其他Polymer 12 PDB declaration: pentameric（5） Consistent with protein copy count	Chain P； UniProt 21–89 Chain Q； UniProt 21–89 Chain R； UniProt 21–89 Chain S； UniProt 21–89 Chain T； UniProt 21–89	Fragment：RECEPTOR-BINDING DOMAIN	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 9 alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose × 3 GAL beta-D-galactopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 2.80 Å R-free 0.226

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 1BOS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C4Q MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE Deposited 1999-08-31	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination 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：F30A, W34A Mutation：F30A, W34A Mutation：F30A, W34A Mutation：F30A, W34A Mutation：F30A, W34A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.52 Å R-free 0.194
1CQF THE COMPLEX OF THE MUTATED SHIGA TOXIN B SUBUNIT AND GB3 TRISACCHARIDE Deposited 1999-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination 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；0.2 M CaCl2, 26% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.200
1D1I MUTATED SHIGA-LIKE TOXIN B SUBUNIT (W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE Deposited 1999-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain B 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain C 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain D 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain E 21–89（69 aa） Fragment：SHIGA 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 7；298 K；10% (NH4)2SO4, 5% propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.211
1D1K MUTATED SHIGA-LIKE TOXIN B SUBUNIT (D17E/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE Deposited 1999-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain B 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain C 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain D 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN Chain E 21–89（69 aa） Fragment：SHIGA TOXIN I BINDING DOMAIN	Mutation：D17E,W34A Mutation：D17E,W34A Mutation：D17E,W34A Mutation：D17E,W34A Mutation：D17E,W34A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.4 M K,NA TARTRATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.218

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

View Construct and Data Evidence

UniProt name	SLTB_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 Author chain F； PDBConstruct 1–69； UniProt 21–89 Author chain G； PDBConstruct 1–69； UniProt 21–89 Author chain H； PDBConstruct 1–69； UniProt 21–89 Author chain I； PDBConstruct 1–69； UniProt 21–89 Author chain J； PDBConstruct 1–69； UniProt 21–89 Author chain K； PDBConstruct 1–69； UniProt 21–89 Author chain L； PDBConstruct 1–69； UniProt 21–89 Author chain M； PDBConstruct 1–69； UniProt 21–89 Author chain N； PDBConstruct 1–69； UniProt 21–89 Author chain O； PDBConstruct 1–69； UniProt 21–89 Author chain P； PDBConstruct 1–69； UniProt 21–89 Author chain Q； PDBConstruct 1–69； UniProt 21–89 Author chain R； PDBConstruct 1–69； UniProt 21–89 Author chain S； PDBConstruct 1–69； UniProt 21–89 Author chain T； 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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bos
Deposition date deposition_date	1998-01-13
Structure title title	SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR
Keywords keywords	TOXIN, RECEPTOR BINDING, PROTEIN-CARBOHYDRATE RECOGNITION, OB-FOLD; 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	46.88 Å
Radius of gyration Rg (electron density) rg_electron	46.29 Å
Forward intensity I(0) i0	486380000.00
Molecular weight molecular_weight	177980.0 kDa
Excluded volume excluded_volume	220880 Å³
Envelope volume envelope_volume	300110 Å³
Hydration-shell volume shell_volume	54860 Å³
Envelope diameter envelope_diameter	148.3 Å
Shell Rg shell_rg	49.92 Å
Envelope Rg envelope_rg	44.74 Å
Shape Rg shape_rg	46.26 Å
Total Rg total_rg	46.52 Å
Total atoms total_atoms	12422
Residues n_residues	1380
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	147.6 Å
Rg (real space) rg_real	46.66 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	4.8640e+08
I(0) uncertainty (real space) i0_real_error	8.8350e+06
Rg (reciprocal space) rg_reciprocal	46.88 Å
I(0) (reciprocal space) i0_reciprocal	486500000.0000
Solution quality estimate total_estimate	0.8887
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.5 Å
Skewness Skewness skewness	-0.003
Kurtosis Kurtosis kurtosis	-0.744
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	34750000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.878

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SHIGA-LIKE TOXIN I B SUBUNIT
Molecular weight formula_weight	7698.6 kDa
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Atom count atom_count	12767

TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR

来源 Source

来源生物 organism	Phage h30, Enterobacteria phage H-19B
通用名 common_name	,
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	33

Entity 3 Entity 3 branched

Description description	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	16

Entity 4 Entity 4 non-polymer

Description description	beta-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	11

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	345

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d1bosa_
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	d1bosb_
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	d1bosc_
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	d1bosd_
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	d1bose_
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	d1bosf_
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	d1bosg_
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	d1bosh_
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	d1bosi_
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	d1bosj_
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	d1bosk_
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	d1bosl_
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	d1bosm_
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	d1bosn_
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	d1boso_
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	d1bosp_
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	d1bosq_
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	d1bosr_
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	d1boss_
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	d1bost_
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

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8. Citations (2)

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Unit-cell length a length_a	127.500 Å
Unit-cell length b length_b	97.700 Å
Unit-cell length c length_c	164.200 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	80

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	21.000 Å
R factor r_factor	0.1700
R_work r_work	0.1700
R_free r_free	0.2260

fit	/app/data/saxs_computation/bo/1bos/1bos.fit
pddf	/app/data/pr_computation/bo/1bos/1bos.pr.out
profile	/app/data/saxs_computation/bo/1bos/1bos.dat