1fnu

STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A

Method: X-RAY DIFFRACTION D_max: 96.3 Å Quality: GOOD

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

EXOTOXIN TYPE A PRECURSOR (ALLELE 1)

OrganismNot specified

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–221 Chain B； UniProt 1–221 Chain C； UniProt 1–221 Chain D； UniProt 1–221	Not recorded	CD CADMIUM ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；0.25 M LiCl, 5-20 mM CdCL2, 4-20% PEG 8000, 50 mM Na acetate, VAPOR DIFFUSION, HANGING DROP	Resolution 1.94 Å R-free 0.281

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 1FNU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B1Z STREPTOCOCCAL PYROGENIC EXOTOXIN A1 Deposited 1998-11-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 33–251（219 aa） Chain B 33–251（219 aa） Chain C 33–251（219 aa） Chain D 33–251（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 8K 17%, AMMONIUM SULPHATE 0.2 M, PH 6.5	Resolution 2.57 Å R-free 0.274
1FNV STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A Deposited 2000-08-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–221（221 aa） Chain B 1–221（221 aa） Chain C 1–221（221 aa） Chain D 1–221（221 aa）	Not recorded	CD CADMIUM ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.25-1 M LiCl, 5-20 mM CdCl2, 4-20% PEG8000, 50 mM Na acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.304
1FNW CRYSTAL STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A Deposited 2000-08-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–221（221 aa） Chain B 1–221（221 aa） Chain C 1–221（221 aa） Chain D 1–221（221 aa）	Not recorded	CD CADMIUM ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.25-1 M LiCl, 5-20 mM CdCl2, 4-20% PEG8000, 50 mM Na acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.90 Å R-free 0.305
1FNW CRYSTAL STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A Deposited 2000-08-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 1–221（221 aa） Chain F 1–221（221 aa） Chain G 1–221（221 aa） Chain H 1–221（221 aa）	Not recorded	CD CADMIUM ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.25-1 M LiCl, 5-20 mM CdCl2, 4-20% PEG8000, 50 mM Na acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.90 Å R-free 0.305

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPEA_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 1–221 Author chain B； PDBConstruct 1–221； UniProt 1–221 Author chain C； PDBConstruct 1–221； UniProt 1–221 Author chain D； PDBConstruct 1–221； UniProt 1–221

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	1fnu
Deposition date deposition_date	2000-08-23
Structure title title	STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A
Keywords keywords	superantigen, exotoxin A, 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	30.58 Å
Radius of gyration Rg (electron density) rg_electron	30.26 Å
Forward intensity I(0) i0	175137000.00
Molecular weight molecular_weight	104980.0 kDa
Excluded volume excluded_volume	130560 Å³
Envelope volume envelope_volume	161680 Å³
Hydration-shell volume shell_volume	43617 Å³
Envelope diameter envelope_diameter	97.2 Å
Shell Rg shell_rg	38.33 Å
Envelope Rg envelope_rg	30.35 Å
Shape Rg shape_rg	30.34 Å
Total Rg total_rg	30.69 Å
Total atoms total_atoms	7307
Residues n_residues	884
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	96.3 Å
Rg (real space) rg_real	30.44 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	1.7510e+08
I(0) uncertainty (real space) i0_real_error	2.6530e+06
Rg (reciprocal space) rg_reciprocal	30.50 Å
I(0) (reciprocal space) i0_reciprocal	175100000.0000
Solution quality estimate total_estimate	0.8939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.9 Å
Skewness Skewness skewness	0.215
Kurtosis Kurtosis kurtosis	-0.371
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26010000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.915

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1fnua1
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.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d1fnua2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

Domain ID domain_id	d1fnub1
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.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d1fnub2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

Domain ID domain_id	d1fnuc1
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.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d1fnuc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

Domain ID domain_id	d1fnud1
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.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d1fnud2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1fnuA01
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	1fnuA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1fnuB01
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	1fnuB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1fnuC01
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	1fnuC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	1fnuD01
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	1fnuD02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

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8. Citations (1)

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Unit-cell length a length_a	55.300 Å
Unit-cell length b length_b	126.800 Å
Unit-cell length c length_c	148.400 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2233
R_free r_free	0.2810

Description description	EXOTOXIN TYPE A PRECURSOR (ALLELE 1)
Molecular weight formula_weight	25862.1 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7934

STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A

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

EXOTOXIN TYPE A PRECURSOR (ALLELE 1)

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	15

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	627

fit	/app/data/saxs_computation/fn/1fnu/1fnu.fit
pddf	/app/data/pr_computation/fn/1fnu/1fnu.pr.out
profile	/app/data/saxs_computation/fn/1fnu/1fnu.dat