1uup

Crystal Structure of A Dimeric Form of Streptococcal Pyrogenic Exotoxin A (SpeA1).

Method: X-RAY DIFFRACTION D_max: 97.2 Å Quality: GOOD

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

EXOTOXIN TYPE A

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–251 Chain D； UniProt 31–251	Fragment：RESIDUES 31-251	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.282
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 31–251 Chain C； UniProt 31–251	Fragment：RESIDUES 31-251	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.50	Resolution 2.60 Å R-free 0.282

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 1UUP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1HA5 Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic exotoxin A (SpeA1): implications for MHC class II recognition. Deposited 2001-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 33–250（218 aa） Fragment：RESIDUES 33-250	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.82 Å R-free 0.283
1L0X TCR beta chain complexed with streptococcal superantigen SpeA Deposited 2002-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 31–251（221 aa）	Mutation：C90S	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG8000, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278
1L0X TCR beta chain complexed with streptococcal superantigen SpeA Deposited 2002-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 31–251（221 aa）	Mutation：C90S	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；15% PEG8000, 0.2M MgCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278
1L0Y T cell receptor beta chain complexed with superantigen SpeA soaked with zinc Deposited 2002-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 31–251（221 aa）	Mutation：C90S	ZN ZINC ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG8K, MgCl, Tris, pH 8., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262
1L0Y T cell receptor beta chain complexed with superantigen SpeA soaked with zinc Deposited 2002-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 31–251（221 aa）	Mutation：C90S	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG8K, MgCl, Tris, pH 8., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.262

3 other PDB entries and 8 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 31–251 Author chain B； PDBConstruct 1–221； UniProt 31–251 Author chain C； PDBConstruct 1–221； UniProt 31–251 Author chain D； PDBConstruct 1–221； UniProt 31–251

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	1uup
Deposition date deposition_date	2004-01-08
Structure title title	Crystal Structure of A Dimeric Form of Streptococcal Pyrogenic Exotoxin A (SpeA1).
Keywords keywords	TOXIN, MOLECULAR RECOGNITION, SUPERANTIGEN, EXOTOXIN, ZINC BINDING, DIMER; 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	30.86 Å
Radius of gyration Rg (electron density) rg_electron	30.14 Å
Forward intensity I(0) i0	163070000.00
Molecular weight molecular_weight	102920.0 kDa
Excluded volume excluded_volume	129080 Å³
Envelope volume envelope_volume	158530 Å³
Hydration-shell volume shell_volume	43027 Å³
Envelope diameter envelope_diameter	98.9 Å
Shell Rg shell_rg	38.17 Å
Envelope Rg envelope_rg	30.17 Å
Shape Rg shape_rg	30.10 Å
Total Rg total_rg	30.94 Å
Total atoms total_atoms	7252
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	97.2 Å
Rg (real space) rg_real	30.72 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.6310e+08
I(0) uncertainty (real space) i0_real_error	2.3800e+06
Rg (reciprocal space) rg_reciprocal	30.78 Å
I(0) (reciprocal space) i0_reciprocal	163100000.0000
Solution quality estimate total_estimate	0.8976
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.1 Å
Skewness Skewness skewness	0.197
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	26410000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.924

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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	EXOTOXIN TYPE A
Molecular weight formula_weight	25820.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7388

QQDPDPSQLHRSSLVKNLQNIYFLYEGDPVTHENVKSVDQLLSHDLIYNVSGPNYDKLKTELKNQEMATLFKDKNVDIYGVEYYHLCYLCENAERSACIYGGVTNHEGNHLEIPKKIVVKVSIDGIQSLSFDIETNKKMVTAQELDYKVRKYLTDNKQLYTNGPSKYETGYIKFIPKNKESFWFDFFPEPEFTQSKYLMIYKDNETLDSNTSQIEVYLTTK

来源 Source

来源生物 organism	STREPTOCOCCUS PYOGENES
NCBI Class编号 ncbi_taxonomy_id	1314
宿主生物 host_organism	ESCHERICHIA COLI BL21

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1uupa1
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	d1uupa2
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	d1uupb1
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	d1uupb2
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	d1uupc1
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	d1uupc2
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	d1uupd1
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	d1uupd2
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	1uupA01
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	1uupA02
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	1uupB01
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	1uupB02
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	1uupC01
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	1uupC02
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	1uupD01
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	1uupD02
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 (2)

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Unit-cell length a length_a	53.300 Å
Unit-cell length b length_b	127.200 Å
Unit-cell length c length_c	148.000 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	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2152
R_work r_work	0.2152
R_free r_free	0.2822

fit	/app/data/saxs_computation/uu/1uup/1uup.fit
pddf	/app/data/pr_computation/uu/1uup/1uup.pr.out
profile	/app/data/saxs_computation/uu/1uup/1uup.dat