4ohj

Crystal structure of toxic shock syndrome toxin-1 (TSST-1) from Staphylococcus aureus

Method: X-RAY DIFFRACTION Dmax: 83.3 Å Quality: GOOD

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

Toxic shock syndrome toxin-1

Staphylococcus aureus

UniProt P06886

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 22–234 Fragment:UNP residues 22-234 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;0.2 M Sodium Chloride, 0.1 M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.28 Å R-free 0.177
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 22–234 Fragment:UNP residues 22-234 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;293 K;0.2 M Sodium Chloride, 0.1 M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.28 Å R-free 0.177

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.

11 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TSST_STAAU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–213; UniProt 22–234 Author chain B; PDBConstruct 1–213; UniProt 22–234

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 4ohj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ohj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ohj
Deposition date deposition_date2014-01-17
Structure title titleCrystal structure of toxic shock syndrome toxin-1 (TSST-1) from Staphylococcus aureus
Keywords keywords;Structural Genomics, NIAID, National Institute of Allergy and Infectious Diseases, Center for Structural Genomics of Infectious Diseases, CSGID, TOXIN ;; TOXIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.22
Radius of gyration Rg (electron density) rg_electron24.24
Forward intensity I(0) i032396800.00
Molecular weight molecular_weight43933.0 kDa
Excluded volume excluded_volume55115 ų
Envelope volume envelope_volume67738 ų
Hydration-shell volume shell_volume24001 ų
Envelope diameter envelope_diameter86.5
Shell Rg shell_rg30.56
Envelope Rg envelope_rg24.39
Shape Rg shape_rg24.21
Total Rg total_rg25.09
Total atoms total_atoms3102
Residues n_residues391
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 dmax83.3
Rg (real space) rg_real25.25
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real3.2400e+07
I(0) uncertainty (real space) i0_real_error4.5030e+05
Rg (reciprocal space) rg_reciprocal25.24
I(0) (reciprocal space) i0_reciprocal32400000.0000
Solution quality estimate total_estimate0.8925
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.4
Skewness Skewness skewness0.364
Kurtosis Kurtosis kurtosis-0.315
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6352000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.983

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4ohja1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.2 — Superantigen toxins, N-terminal domain
Domain ID domain_idd4ohja2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.6 — Superantigen toxins, C-terminal domain
Family Family familyd.15.6.1 — Superantigen toxins, C-terminal domain
Domain ID domain_idd4ohja3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4ohjb1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.2 — Superantigen toxins, N-terminal domain
Domain ID domain_idd4ohjb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.6 — Superantigen toxins, C-terminal domain
Family Family familyd.15.6.1 — Superantigen toxins, C-terminal domain
Domain ID domain_idd4ohjb3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id4ohjA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily120
Domain ID domain_id4ohjA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id4ohjB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily120
Domain ID domain_id4ohjB02
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)