1czw

STRUCTURE OF THE W34A MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT

Method: X-RAY DIFFRACTION D_max: 106.9 Å Quality: GOOD

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

SHIGA TOXIN B-CHAIN

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：SHIGA-LIKE TOXIN I BINDING DOMAIN Mutation：W34A	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 5 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：SHIGA-LIKE TOXIN I BINDING DOMAIN Mutation：W34A	No other associated polymer	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

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 1CZW	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 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 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：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
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 3 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

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	1czw
Deposition date deposition_date	1999-09-07
Structure title title	STRUCTURE OF THE W34A MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT
Keywords keywords	BACTERIAL TOXIN, SUGAR RECEPTOR BINDING DOMAIN, PROTEIN-CARBOHYDRATE RECOGNITION, OB-FOLD, 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	32.35 Å
Radius of gyration Rg (electron density) rg_electron	31.90 Å
Forward intensity I(0) i0	94776100.00
Molecular weight molecular_weight	75745.0 kDa
Excluded volume excluded_volume	94164 Å³
Envelope volume envelope_volume	119610 Å³
Hydration-shell volume shell_volume	32615 Å³
Envelope diameter envelope_diameter	107.0 Å
Shell Rg shell_rg	37.52 Å
Envelope Rg envelope_rg	31.25 Å
Shape Rg shape_rg	31.86 Å
Total Rg total_rg	32.52 Å
Total atoms total_atoms	5310
Residues n_residues	690
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	106.9 Å
Rg (real space) rg_real	32.46 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	9.4780e+07
I(0) uncertainty (real space) i0_real_error	1.5120e+06
Rg (reciprocal space) rg_reciprocal	32.42 Å
I(0) (reciprocal space) i0_reciprocal	94770000.0000
Solution quality estimate total_estimate	0.8835
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.1 Å
Skewness Skewness skewness	0.380
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9518000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.865

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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) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1czwa_
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	d1czwb_
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	d1czwc_
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	d1czwd_
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	d1czwe_
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	d1czwf_
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	d1czwg_
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	d1czwh_
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	d1czwi_
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	d1czwj_
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 (10 domains)

Domain ID domain_id	1czwA00
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	1czwB00
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	1czwC00
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	1czwD00
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	1czwE00
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	1czwF00
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	1czwG00
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	1czwH00
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	1czwI00
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	1czwJ00
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	107.550 Å
Unit-cell length b length_b	108.920 Å
Unit-cell length c length_c	57.350 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	40

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	48.600 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2140

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	10

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	5574

STRUCTURE OF THE W34A MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT

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

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) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

8. Citations (1)

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	264

fit	/app/data/saxs_computation/cz/1czw/1czw.fit
pddf	/app/data/pr_computation/cz/1czw/1czw.pr.out
profile	/app/data/saxs_computation/cz/1czw/1czw.dat