1dm0

SHIGA TOXIN

Method: X-RAY DIFFRACTION Dmax: 142.6 Å Quality: GOOD

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

SHIGA TOXIN A SUBUNIT

Shigella dysenteriae

UniProt Q7BQ99

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 23–309 Not recorded SHIGA TOXIN B SUBUNIT × 5 (Q7BQ98) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain L; UniProt 23–309 Not recorded SHIGA TOXIN B SUBUNIT × 5 (Q7BQ98) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å
3 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain A; UniProt 23–309 Chain L; UniProt 23–309 Not recorded SHIGA TOXIN B SUBUNIT × 10 (Q7BQ98) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å

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.

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

View Construct and Data Evidence
UniProt name Q7BQ99_SHIDY
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–287; UniProt 23–309 Author chain L; PDBConstruct 1–287; UniProt 23–309

SHIGA TOXIN B SUBUNIT

Shigella dysenteriae

UniProt Q7BQ98

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 21–89 Chain C; UniProt 21–89 Chain D; UniProt 21–89 Chain E; UniProt 21–89 Chain F; UniProt 21–89 Not recorded SHIGA TOXIN A SUBUNIT × 1 (Q7BQ99) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å
2 Protein heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 21–89 Chain H; UniProt 21–89 Chain I; UniProt 21–89 Chain J; UniProt 21–89 Chain K; UniProt 21–89 Not recorded SHIGA TOXIN A SUBUNIT × 1 (Q7BQ99) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å
3 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric(12) Consistent with protein copy count Chain B; UniProt 21–89 Chain C; UniProt 21–89 Chain D; UniProt 21–89 Chain E; UniProt 21–89 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 Chain K; UniProt 21–89 Not recorded SHIGA TOXIN A SUBUNIT × 2 (Q7BQ99) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5;294 K;sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 2.50 Å

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.

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

View Construct and Data Evidence
UniProt name Q7BQ98_SHIDY
Isoform
PDB entities 2
Chains and sequence ranges 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 Author chain K; 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

SAXS profile for 1dm0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dm0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dm0
Deposition date deposition_date1999-12-13
Structure title titleSHIGA TOXIN
Keywords keywordsAB5 STRUCTURE, POLYPEPTIDE A, BLOCKING, ACTIVE SITE, TOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.89
Radius of gyration Rg (electron density) rg_electron38.15
Forward intensity I(0) i0282299000.00
Molecular weight molecular_weight134860.0 kDa
Excluded volume excluded_volume168170 ų
Envelope volume envelope_volume208560 ų
Hydration-shell volume shell_volume49446 ų
Envelope diameter envelope_diameter153.6
Shell Rg shell_rg40.25
Envelope Rg envelope_rg38.32
Shape Rg shape_rg38.14
Total Rg total_rg38.30
Total atoms total_atoms9476
Residues n_residues1216
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 dmax142.6
Rg (real space) rg_real38.40
Rg uncertainty (real space) rg_real_error1.56
I(0) (real space) i0_real2.8230e+08
I(0) uncertainty (real space) i0_real_error4.7980e+06
Rg (reciprocal space) rg_reciprocal38.08
I(0) (reciprocal space) i0_reciprocal282200000.0000
Solution quality estimate total_estimate0.7859
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.3
Skewness Skewness skewness0.763
Kurtosis Kurtosis kurtosis0.425
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48570000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.508; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.860; Smooth: 0.830

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1dm0a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.2 — Shiga toxin, A-chain
Domain ID domain_idd1dm0b_
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_idd1dm0c_
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_idd1dm0d_
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_idd1dm0e_
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_idd1dm0f_
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_idd1dm0g_
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_idd1dm0h_
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_idd1dm0i_
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_idd1dm0j_
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_idd1dm0k_
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_idd1dm0l_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.2 — Shiga toxin, A-chain

CATH v4.4 (14 domains)

Domain ID domain_id1dm0A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id1dm0A02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
Domain ID domain_id1dm0B00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0C00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0D00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0E00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0F00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0G00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0H00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0I00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0J00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0K00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily70
Domain ID domain_id1dm0L01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id1dm0L02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2

8. Citations (3)

9. Files and Curves (10)