1b1z

STREPTOCOCCAL PYROGENIC EXOTOXIN A1

Method: X-RAY DIFFRACTION D_max: 97.8 Å Quality: GOOD

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

PROTEIN (TOXIN)

Streptococcus pyogenes

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 33–251 Chain B； UniProt 33–251 Chain C； UniProt 33–251 Chain D； UniProt 33–251	Not recorded	No other associated polymer	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

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 1B1Z	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FNU STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A Deposited 2000-08-23	Different construct 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 × 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
1FNV STRUCTURE OF STREPTOCOCCAL PYROGENIC EXOTOXIN A Deposited 2000-08-23	Different construct 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 construct 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 construct 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 1–219； UniProt 33–251 Author chain B； PDBConstruct 1–219； UniProt 33–251 Author chain C； PDBConstruct 1–219； UniProt 33–251 Author chain D； PDBConstruct 1–219； UniProt 33–251

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	1b1z
Deposition date deposition_date	1998-11-24
Structure title title	STREPTOCOCCAL PYROGENIC EXOTOXIN A1
Keywords keywords	SUPERANTIGEN, ZINC BINDING, PYROGENIC EXOTOXIN, 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	30.66 Å
Radius of gyration Rg (electron density) rg_electron	30.03 Å
Forward intensity I(0) i0	150418000.00
Molecular weight molecular_weight	99494.0 kDa
Excluded volume excluded_volume	125140 Å³
Envelope volume envelope_volume	151640 Å³
Hydration-shell volume shell_volume	41680 Å³
Envelope diameter envelope_diameter	98.1 Å
Shell Rg shell_rg	37.78 Å
Envelope Rg envelope_rg	29.90 Å
Shape Rg shape_rg	30.01 Å
Total Rg total_rg	30.77 Å
Total atoms total_atoms	7027
Residues n_residues	872
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	97.8 Å
Rg (real space) rg_real	30.52 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	1.5040e+08
I(0) uncertainty (real space) i0_real_error	2.3260e+06
Rg (reciprocal space) rg_reciprocal	30.58 Å
I(0) (reciprocal space) i0_reciprocal	150400000.0000
Solution quality estimate total_estimate	0.8949
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.5 Å
Skewness Skewness skewness	0.193
Kurtosis Kurtosis kurtosis	-0.405
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	25000000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.947

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1b1za1
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	d1b1za2
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	d1b1zb1
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	d1b1zb2
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	d1b1zc1
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	d1b1zc2
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	d1b1zd1
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	d1b1zd2
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	1b1zA01
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	1b1zA02
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	1b1zB01
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	1b1zB02
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	1b1zC01
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	1b1zC02
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	1b1zD01
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	1b1zD02
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	127.400 Å
Unit-cell length b length_b	101.000 Å
Unit-cell length c length_c	81.800 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.570 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2740

Description description	PROTEIN (TOXIN)
Molecular weight formula_weight	25563.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7114

STREPTOCOCCAL PYROGENIC EXOTOXIN A1

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

PROTEIN (TOXIN)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 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)

来源生物 organism	Streptococcus pyogenes
NCBI Class编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

fit	/app/data/saxs_computation/b1/1b1z/1b1z.fit
pddf	/app/data/pr_computation/b1/1b1z/1b1z.pr.out
profile	/app/data/saxs_computation/b1/1b1z/1b1z.dat