5ele

Cholera toxin El Tor B-pentamer in complex with A Lewis-y

Method: X-RAY DIFFRACTION Dmax: 91.1 Å Quality: EXCELLENT

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

Cholera enterotoxin subunit B

Vibrio cholerae O1

UniProt P01556

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 1 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 22–124 Chain B; UniProt 22–124 Chain C; UniProt 22–124 Chain D; UniProt 22–124 Chain E; UniProt 22–124 Not recorded ;alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose ; × 1 CA CALCIUM ION × 10 FUC alpha-L-fucopyranose × 1 BCN BICINE × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;0.1 M Bicine-Tris, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride Resolution 1.60 Å R-free 0.226
2 Other combination Homooligomer Protein × 5 其他Polymer 2 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 22–124 Chain G; UniProt 22–124 Chain H; UniProt 22–124 Chain I; UniProt 22–124 Chain J; UniProt 22–124 Not recorded ;alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose ; × 2 FUC alpha-L-fucopyranose × 3 1PE PENTAETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;293 K;0.1 M Bicine-Tris, 9% PEG1000, 9% PEG3350, 9% MPD, 0.03 M calcium chloride, 0.03 M magnesium chloride Resolution 1.60 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.

26 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CHTB_VIBCH
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–103; UniProt 22–124 Author chain B; PDBConstruct 1–103; UniProt 22–124 Author chain C; PDBConstruct 1–103; UniProt 22–124 Author chain D; PDBConstruct 1–103; UniProt 22–124 Author chain E; PDBConstruct 1–103; UniProt 22–124 Author chain F; PDBConstruct 1–103; UniProt 22–124 Author chain G; PDBConstruct 1–103; UniProt 22–124 Author chain H; PDBConstruct 1–103; UniProt 22–124 Author chain I; PDBConstruct 1–103; UniProt 22–124 Author chain J; PDBConstruct 1–103; UniProt 22–124

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

SAXS profile for 5ele

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ele
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ele
Deposition date deposition_date2015-11-04
Structure title titleCholera toxin El Tor B-pentamer in complex with A Lewis-y
Keywords keywordsCholera toxin B-pentamer, A Lewis-y, complex, blood group oligosaccharide/antigen, toxin; TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.93
Radius of gyration Rg (electron density) rg_electron29.42
Forward intensity I(0) i0233114000.00
Molecular weight molecular_weight122040.0 kDa
Excluded volume excluded_volume153160 ų
Envelope volume envelope_volume180750 ų
Hydration-shell volume shell_volume48528 ų
Envelope diameter envelope_diameter92.2
Shell Rg shell_rg38.77
Envelope Rg envelope_rg29.28
Shape Rg shape_rg29.46
Total Rg total_rg30.10
Total atoms total_atoms8530
Residues n_residues1030
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax91.1
Rg (real space) rg_real30.68
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real2.3310e+08
I(0) uncertainty (real space) i0_real_error3.0910e+06
Rg (reciprocal space) rg_reciprocal30.78
I(0) (reciprocal space) i0_reciprocal233100000.0000
Solution quality estimate total_estimate0.9071
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.9
Skewness Skewness skewness0.044
Kurtosis Kurtosis kurtosis-0.558
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha148500000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.963

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd5elea_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5eleb_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5elec_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5eled_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5elee_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5elef_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5eleg_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5eleh_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5elei_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits
Domain ID domain_idd5elej_
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.1 — Bacterial AB5 toxins, B-subunits

CATH v4.4 (10 domains)

Domain ID domain_id5eleA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleC00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleD00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleE00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleF00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleG00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleH00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleI00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id5eleJ00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110

8. Citations (1)

9. Files and Curves (10)