SAXSdb — 1d1i

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

SHIGA TOXIN B-CHAIN

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 5 其他Polymer 6	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose × 1 alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose × 5 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

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

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	1d1i
Deposition date deposition_date	1999-09-17
Structure title title	MUTATED SHIGA-LIKE TOXIN B SUBUNIT (W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE
Keywords keywords	TOXIN, RECEPTOR BINDING, PROTEIN-CARBOHYDRATE RECOGNITION, OB-FOLD; TOXIN
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.

1d1i__assembly_1__model_1

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

Download this curve (.dat)

1d1i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d1i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.78 Å
Rg (electron density)	21.54 Å
Total Rg	22.45 Å
Atom count	2848
Residues	345
Excluded volume	50579 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d1i__assembly_1__model_1`	pentameric （5）	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 (4)

Entity 1 Entity 1 polymer

Description description	SHIGA TOXIN B-CHAIN
Molecular weight formula_weight	7583.5 kDa
Mutation mutation	W34A
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	3044

TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 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	1

Entity 3 Entity 3 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	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1d1ia_
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	d1d1ib_
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	d1d1ic_
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	d1d1id_
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	d1d1ie_
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	1d1iA00
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	1d1iB00
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	1d1iC00
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	1d1iD00
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	1d1iE00
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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Unit-cell length a length_a	44.232 Å
Unit-cell length b length_b	44.136 Å
Unit-cell length c length_c	53.881 Å
Unit-cell angle α angle_alpha	106.04 °
Unit-cell angle β angle_beta	106.37 °
Unit-cell angle γ angle_gamma	99.22 °
Molecules per unit cell Z z_pdb	5

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	19.700 Å
R factor r_factor	—
R_work r_work	0.1910
R_free r_free	0.2110

MUTATED SHIGA-LIKE TOXIN B SUBUNIT (W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE

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

SHIGA TOXIN B-CHAIN

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

1d1i__assembly_1__model_1

1d1i__assembly_1__model_1 | I(q)

1d1i__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

MUTATED SHIGA-LIKE TOXIN B SUBUNIT (W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE

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

SHIGA TOXIN B-CHAIN

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

1d1i__assembly_1__model_1

1d1i__assembly_1__model_1 | I(q)

1d1i__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)