SAXSdb — 1c48

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

PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)

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	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：RECEPTOR-BINDING DOMAIN Mutation：G62T	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 1.60 Å R-free 0.240

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 1C48	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CZG STRUCTURE OF THE G62T MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT Deposited 1999-09-03	Different construct 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 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 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
2XSC Crystal structure of the cell-binding B oligomer of verotoxin-1 from E. coli Deposited 2010-09-27	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：RESIDUES 21-89 Chain B 21–89（69 aa） Fragment：RESIDUES 21-89 Chain C 21–89（69 aa） Fragment：RESIDUES 21-89 Chain D 21–89（69 aa） Fragment：RESIDUES 21-89 Chain E 21–89（69 aa） Fragment：RESIDUES 21-89	Not recorded	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

3 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

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	1c48
Deposition date deposition_date	1999-08-11
Structure title title	MUTATED SHIGA-LIKE TOXIN B SUBUNIT (G62T)
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	22.19 Å
Radius of gyration Rg (electron density) rg_electron	20.86 Å
Forward intensity I(0) i0	25844400.00
Molecular weight molecular_weight	38669.0 kDa
Excluded volume excluded_volume	48198 Å³
Envelope volume envelope_volume	54247 Å³
Hydration-shell volume shell_volume	21784 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	27.26 Å
Envelope Rg envelope_rg	20.74 Å
Shape Rg shape_rg	20.81 Å
Total Rg total_rg	21.77 Å
Total atoms total_atoms	2715
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	22.06 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	2.5840e+07
I(0) uncertainty (real space) i0_real_error	3.3360e+05
Rg (reciprocal space) rg_reciprocal	22.08 Å
I(0) (reciprocal space) i0_reciprocal	25840000.0000
Solution quality estimate total_estimate	0.7124
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.592
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7448000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.999; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1c48a_
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	d1c48b_
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	d1c48c_
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	d1c48d_
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	d1c48e_
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	1c48A00
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	1c48B00
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	1c48C00
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	1c48D00
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	1c48E00
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 (2)

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Unit-cell length a length_a	93.972 Å
Unit-cell length b length_b	61.928 Å
Unit-cell length c length_c	60.327 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	55.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2400

Description description	PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)
Molecular weight formula_weight	7742.7 kDa
Mutation mutation	G62T
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	3127

MUTATED SHIGA-LIKE TOXIN B SUBUNIT (G62T)

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

PROTEIN (SHIGA-LIKE TOXIN I B SUBUNIT)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Phage h30
NCBI Class编号 ncbi_taxonomy_id	12371
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	348

fit	/app/data/saxs_computation/c4/1c48/1c48.fit
pddf	/app/data/pr_computation/c4/1c48/1c48.pr.out
profile	/app/data/saxs_computation/c4/1c48/1c48.dat