SAXSdb — 1ck1

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

PROTEIN (ENTEROTOXIN TYPE C-3)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–239	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；100MM PHOSPHATE (PH7.4) 2.4M AMMONIUM SULFATE 1.25% PEG400, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.233

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	Q06535_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–239； UniProt 1–239

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	1ck1
Deposition date deposition_date	1999-04-26
Structure title title	STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN C3
Keywords keywords	STAPHYLOCOCCAL ENTEROTOXIN, SUPERANTIGEN, ZINC, 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	19.22 Å
Radius of gyration Rg (electron density) rg_electron	17.96 Å
Forward intensity I(0) i0	13952400.00
Molecular weight molecular_weight	27689.0 kDa
Excluded volume excluded_volume	34471 Å³
Envelope volume envelope_volume	40551 Å³
Hydration-shell volume shell_volume	18675 Å³
Envelope diameter envelope_diameter	60.3 Å
Shell Rg shell_rg	24.29 Å
Envelope Rg envelope_rg	18.22 Å
Shape Rg shape_rg	17.93 Å
Total Rg total_rg	18.98 Å
Total atoms total_atoms	1945
Residues n_residues	239
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	59.6 Å
Rg (real space) rg_real	19.10 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.3950e+07
I(0) uncertainty (real space) i0_real_error	1.6140e+05
Rg (reciprocal space) rg_reciprocal	19.12 Å
I(0) (reciprocal space) i0_reciprocal	13950000.0000
Solution quality estimate total_estimate	0.9051
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.0 Å
Skewness Skewness skewness	0.131
Kurtosis Kurtosis kurtosis	-0.494
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2655000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.997

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ck1a1
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	d1ck1a2
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 (2 domains)

Domain ID domain_id	1ck1A01
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	1ck1A02
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	43.700 Å
Unit-cell length b length_b	43.700 Å
Unit-cell length c length_c	280.500 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	8

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1620
R_free r_free	0.2330

Description description	PROTEIN (ENTEROTOXIN TYPE C-3)
Molecular weight formula_weight	27664.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2028

STRUCTURE OF STAPHYLOCOCCAL ENTEROTOXIN C3

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

PROTEIN (ENTEROTOXIN TYPE C-3)

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	83

fit	/app/data/saxs_computation/ck/1ck1/1ck1.fit
pddf	/app/data/pr_computation/ck/1ck1/1ck1.pr.out
profile	/app/data/saxs_computation/ck/1ck1/1ck1.dat