SAXSdb — 1cby

▼

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

DELTA-ENDOTOXIN CYTB

Bacillus thuringiensis serovar kyushuensis

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 1–259	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.60 Å R-free 0.261

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	CT2AA_BACTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–259； UniProt 1–259

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cby
Deposition date deposition_date	1995-09-05
Structure title title	DELTA-ENDOTOXIN
Keywords keywords	MOSQUITOCIDAL, MEMBRANE PORE, CYTOLYTIC, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.41 Å
Radius of gyration Rg (electron density) rg_electron	18.13 Å
Forward intensity I(0) i0	10716900.00
Molecular weight molecular_weight	25540.0 kDa
Excluded volume excluded_volume	32520 Å³
Envelope volume envelope_volume	38890 Å³
Hydration-shell volume shell_volume	18160 Å³
Envelope diameter envelope_diameter	69.1 Å
Shell Rg shell_rg	24.15 Å
Envelope Rg envelope_rg	18.61 Å
Shape Rg shape_rg	18.08 Å
Total Rg total_rg	19.30 Å
Total atoms total_atoms	1807
Residues n_residues	227
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.5 Å
Rg (real space) rg_real	19.37 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.0720e+07
I(0) uncertainty (real space) i0_real_error	1.4060e+05
Rg (reciprocal space) rg_reciprocal	19.38 Å
I(0) (reciprocal space) i0_reciprocal	10720000.0000
Solution quality estimate total_estimate	0.8563
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.340
Kurtosis Kurtosis kurtosis	-0.128
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2799000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.724; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.987

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cbya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.103 — CytB endotoxin-like
Superfamily Superfamily superfamily	d.103.1 — CytB endotoxin-like
Family Family family	d.103.1.1 — CytB endotoxin-like

CATH v4.4 (1 domains)

Domain ID domain_id	1cbyA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	198 — Delta-endotoxin CytB
Homologous superfamily homologous superfamily	10 — Delta-endotoxin CytB-like

▶

8. Citations (4)

▶

Unit-cell length a length_a	66.810 Å
Unit-cell length b length_b	66.810 Å
Unit-cell length c length_c	170.790 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	19.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2610

Description description	DELTA-ENDOTOXIN CYTB
Molecular weight formula_weight	29260.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1840

DELTA-ENDOTOXIN

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

DELTA-ENDOTOXIN CYTB

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (4)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus thuringiensis serovar kyushuensis
NCBI Class编号 ncbi_taxonomy_id	44161
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	28

fit	/app/data/saxs_computation/cb/1cby/1cby.fit
pddf	/app/data/pr_computation/cb/1cby/1cby.pr.out
profile	/app/data/saxs_computation/cb/1cby/1cby.dat