SAXSdb — 1d1k

▼

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

SHIGA-LIKE TOXIN I SUBUNIT B

Phage h30

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 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：SHIGA TOXIN I BINDING DOMAIN Mutation：D17E,W34A	alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose × 5	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

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 1D1K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BOS SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR Deposited 1998-01-13	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：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	Not recorded	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
1BOS SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR Deposited 1998-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain F 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain G 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain H 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain I 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain J 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN	Not recorded	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
1BOS SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR Deposited 1998-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain K 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain L 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain M 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain N 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain O 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN	Not recorded	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
1BOS SHIGA-LIKE TOXIN COMPLEXED WITH ITS RECEPTOR Deposited 1998-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Homooligomer；Protein × 5 PDB declaration: pentameric	Chain P 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain Q 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain R 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain S 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN Chain T 21–89（69 aa） Fragment：RECEPTOR-BINDING DOMAIN	Not recorded	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
1C4Q MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE Deposited 1999-08-31	Different construct Different mutation/modification 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 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 mutation/modification Different oligomeric state 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

4 other PDB entries and 7 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

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1d1k
Deposition date deposition_date	1999-09-17
Structure title title	MUTATED SHIGA-LIKE TOXIN B SUBUNIT (D17E/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE
Keywords keywords	TOXIN, RECEPTOR BINDING, PROTEIN-CARBOHYDRATE RECOGNITION, OB-FOLD; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.74 Å
Radius of gyration Rg (electron density) rg_electron	21.47 Å
Forward intensity I(0) i0	28763200.00
Molecular weight molecular_weight	40475.0 kDa
Excluded volume excluded_volume	50296 Å³
Envelope volume envelope_volume	57629 Å³
Hydration-shell volume shell_volume	22412 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	28.08 Å
Envelope Rg envelope_rg	21.27 Å
Shape Rg shape_rg	21.42 Å
Total Rg total_rg	22.39 Å
Total atoms total_atoms	2830
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

▼

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

Maximum dimension Dmax dmax	67.7 Å
Rg (real space) rg_real	22.62 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	2.8760e+07
I(0) uncertainty (real space) i0_real_error	3.8210e+05
Rg (reciprocal space) rg_reciprocal	22.65 Å
I(0) (reciprocal space) i0_reciprocal	28760000.0000
Solution quality estimate total_estimate	0.9149
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.8 Å
Skewness Skewness skewness	0.114
Kurtosis Kurtosis kurtosis	-0.612
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7417000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.974; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.970

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SHIGA-LIKE TOXIN I SUBUNIT B
Molecular weight formula_weight	7597.5 kDa
Mutation mutation	D17E,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	3076

TPDCVTGKVEYTKYNDEDTFTVKVGDKELFTNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR

来源 Source

来源生物 organism	Phage h30
NCBI Class编号 ncbi_taxonomy_id	12371
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)-alpha-D-glucopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	246

▼

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1d1ka_
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	d1d1kb_
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	d1d1kc_
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	d1d1kd_
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	d1d1ke_
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	1d1kA00
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	1d1kB00
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	1d1kC00
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	1d1kD00
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	1d1kE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	70 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	44.223 Å
Unit-cell length b length_b	44.131 Å
Unit-cell length c length_c	53.710 Å
Unit-cell angle α angle_alpha	106.05 °
Unit-cell angle β angle_beta	106.38 °
Unit-cell angle γ angle_gamma	99.26 °
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	2.000 Å
Low-resolution limit resolution_low	25.800 Å
R factor r_factor	—
R_work r_work	0.1930
R_free r_free	0.2180

fit	/app/data/saxs_computation/d1/1d1k/1d1k.fit
pddf	/app/data/pr_computation/d1/1d1k/1d1k.pr.out
profile	/app/data/saxs_computation/d1/1d1k/1d1k.dat

MUTATED SHIGA-LIKE TOXIN B SUBUNIT (D17E/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE

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

SHIGA-LIKE TOXIN I 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