SAXSdb — 1bxt

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

PROTEIN (STREPTOCOCCAL SUPERANTIGEN)

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 27–260 Chain B； UniProt 27–260	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 1.85 Å R-free 0.263

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q54971_STRPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 27–260 Author chain B； PDBConstruct 1–234； UniProt 27–260

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bxt
Deposition date deposition_date	1998-10-08
Structure title title	STREPTOCOCCAL SUPERANTIGEN (SSA) FROM STREPTOCOCCUS PYOGENES
Keywords keywords	BACTERIAL SUPERANTIGEN, MHC CLASS II INTERACTION, T CELL ACTIVATION, TOXIC SHOCK-LIKE SYNDROME, IMMUNE SYSTEM; IMMUNE SYSTEM
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	28.94 Å
Radius of gyration Rg (electron density) rg_electron	28.51 Å
Forward intensity I(0) i0	42920600.00
Molecular weight molecular_weight	51064.0 kDa
Excluded volume excluded_volume	63758 Å³
Envelope volume envelope_volume	78862 Å³
Hydration-shell volume shell_volume	24306 Å³
Envelope diameter envelope_diameter	98.4 Å
Shell Rg shell_rg	33.80 Å
Envelope Rg envelope_rg	28.46 Å
Shape Rg shape_rg	28.50 Å
Total Rg total_rg	29.07 Å
Total atoms total_atoms	3596
Residues n_residues	446
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	93.9 Å
Rg (real space) rg_real	29.15 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	4.2920e+07
I(0) uncertainty (real space) i0_real_error	6.3970e+05
Rg (reciprocal space) rg_reciprocal	29.06 Å
I(0) (reciprocal space) i0_reciprocal	42920000.0000
Solution quality estimate total_estimate	0.8343
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.454
Kurtosis Kurtosis kurtosis	-0.594
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6715000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.699; Smooth: 0.791

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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) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bxta1
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	d1bxta2
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	d1bxtb1
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	d1bxtb2
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 (4 domains)

Domain ID domain_id	1bxtA01
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	1bxtA02
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	1bxtB01
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	1bxtB02
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	81.900 Å
Unit-cell length b length_b	84.550 Å
Unit-cell length c length_c	144.010 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2630

Description description	PROTEIN (STREPTOCOCCAL SUPERANTIGEN)
Molecular weight formula_weight	26954.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3970

STREPTOCOCCAL SUPERANTIGEN (SSA) FROM STREPTOCOCCUS PYOGENES

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

PROTEIN (STREPTOCOCCAL SUPERANTIGEN)

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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	374

fit	/app/data/saxs_computation/bx/1bxt/1bxt.fit
pddf	/app/data/pr_computation/bx/1bxt/1bxt.pr.out
profile	/app/data/saxs_computation/bx/1bxt/1bxt.dat