2o2l

Crystal structure of human heat-labile enterotoxin in complex with a blood group A antigen analog

Method: X-RAY DIFFRACTION D_max: 124.8 Å Quality: GOOD

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

Heat-labile enterotoxin B chain

Escherichia coli

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 D； UniProt 22–124 Chain E； UniProt 22–124 Chain F； UniProt 22–124 Chain G； UniProt 22–124 Chain H； 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)]beta-D-glucopyranose ; × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.53 Å R-free 0.237
2	Other combination Homooligomer Protein × 5 其他Polymer 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain I； UniProt 22–124 Chain J； UniProt 22–124 Chain K； UniProt 22–124 Chain L； UniProt 22–124 Chain M； 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)]beta-D-glucopyranose ; × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.53 Å R-free 0.237

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 2O2L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B44 CRYSTAL STRUCTURE OF THE B SUBUNIT OF HEAT-LABILE ENTEROTOXIN FROM E. COLI CARRYING A PEPTIDE WITH ANTI-HSV ACTIVITY Deposited 1999-01-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain D 22–124（103 aa） Fragment：SUBUNIT B Chain E 22–124（103 aa） Fragment：SUBUNIT B Chain F 22–124（103 aa） Fragment：SUBUNIT B Chain G 22–124（103 aa） Fragment：SUBUNIT B Chain H 22–124（103 aa） Fragment：SUBUNIT B	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 3.30 Å R-free 0.255
1LTR CRYSTAL STRUCTURE OF THE B SUBUNIT OF HUMAN HEAT-LABILE ENTEROTOXIN FROM E. COLI CARRYING A PEPTIDE WITH ANTI-HSV ACTIVITY Deposited 1998-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain D 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain E 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain F 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain G 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain H 22–123（102 aa） Fragment：SUBUNIT B-R2	Mutation：N103K Mutation：N103K Mutation：N103K Mutation：N103K Mutation：N103K	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 3.04 Å R-free 0.217
1LTR CRYSTAL STRUCTURE OF THE B SUBUNIT OF HUMAN HEAT-LABILE ENTEROTOXIN FROM E. COLI CARRYING A PEPTIDE WITH ANTI-HSV ACTIVITY Deposited 1998-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain D 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain E 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain F 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain G 22–123（102 aa） Fragment：SUBUNIT B-R2 Chain H 22–123（102 aa） Fragment：SUBUNIT B-R2	Mutation：N103K Mutation：N103K Mutation：N103K Mutation：N103K Mutation：N103K	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6	Resolution 3.04 Å R-free 0.217

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ELBH_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	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 Author chain K； PDBConstruct 1–103； UniProt 22–124 Author chain L； PDBConstruct 1–103； UniProt 22–124 Author chain M； 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

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	2o2l
Deposition date deposition_date	2006-11-30
Structure title title	Crystal structure of human heat-labile enterotoxin in complex with a blood group A antigen analog
Keywords keywords	Enterotoxigenic E. coli, heat-labile enterotoxin, blood group antigen, 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	37.24 Å
Radius of gyration Rg (electron density) rg_electron	36.69 Å
Forward intensity I(0) i0	230794000.00
Molecular weight molecular_weight	123540.0 kDa
Excluded volume excluded_volume	155030 Å³
Envelope volume envelope_volume	192310 Å³
Hydration-shell volume shell_volume	44315 Å³
Envelope diameter envelope_diameter	125.1 Å
Shell Rg shell_rg	42.07 Å
Envelope Rg envelope_rg	36.34 Å
Shape Rg shape_rg	36.70 Å
Total Rg total_rg	36.98 Å
Total atoms total_atoms	8615
Residues n_residues	1012
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	124.8 Å
Rg (real space) rg_real	37.42 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	2.3080e+08
I(0) uncertainty (real space) i0_real_error	3.8850e+06
Rg (reciprocal space) rg_reciprocal	37.31 Å
I(0) (reciprocal space) i0_reciprocal	230800000.0000
Solution quality estimate total_estimate	0.8722
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.7 Å
Skewness Skewness skewness	0.386
Kurtosis Kurtosis kurtosis	-0.602
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38000000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.905

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Heat-labile enterotoxin B chain
Molecular weight formula_weight	11731.4 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,G,H,I,J,K,L,M
Atom count atom_count	8893

APQSITELCSEYHNTQIYTINDKILSYTESMAGKREMVIITFKSGATFQVEVPGSQHIDSQKKAIERMKDTLRITYLTETKIDKLCVWNNKTPNSIAAISMEK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Vibrio cholerae

Entity 2 Entity 2 branched

Description description	;alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]beta-D-glucopyranose ;
Molecular weight formula_weight	837.8 kDa
Source method src_method	man
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	278

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2o2ld_
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	d2o2le_
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	d2o2lf_
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	d2o2lg_
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	d2o2lh_
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	d2o2li_
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	d2o2lj_
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	d2o2lk_
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	d2o2ll_
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	d2o2lm_
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	2o2lD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lG00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lH00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lI00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lJ00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lK00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lL00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	2o2lM00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

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8. Citations (1)

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Unit-cell length a length_a	117.799 Å
Unit-cell length b length_b	166.965 Å
Unit-cell length c length_c	57.478 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	2.530 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1835
R_work r_work	0.1807
R_free r_free	0.2370

fit	/app/data/saxs_computation/o2/2o2l/2o2l.fit
pddf	/app/data/pr_computation/o2/2o2l/2o2l.pr.out
profile	/app/data/saxs_computation/o2/2o2l/2o2l.dat