SAXSdb — 1b7d

▼

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

PROTEIN (NEUROTOXIN TS1)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–81	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；pH 6.0	Resolution 1.73 Å R-free 0.238

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 1B7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NPI Tityus Serrulatus Neurotoxin (Ts1) at atomic resolution Deposited 2003-01-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–81（61 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 6000, potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.16 Å R-free 0.139

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SCX7_TITSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–61； UniProt 21–81

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	1b7d
Deposition date deposition_date	1999-01-21
Structure title title	NEUROTOXIN (TS1) FROM BRAZILIAN SCORPION TITYUS SERRULATUS
Keywords keywords	LONG-CHAIN NEUROTOXIN, 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	12.26 Å
Radius of gyration Rg (electron density) rg_electron	11.16 Å
Forward intensity I(0) i0	1269290.00
Molecular weight molecular_weight	6990.0 kDa
Excluded volume excluded_volume	8530 Å³
Envelope volume envelope_volume	9810 Å³
Hydration-shell volume shell_volume	7838 Å³
Envelope diameter envelope_diameter	37.4 Å
Shell Rg shell_rg	16.18 Å
Envelope Rg envelope_rg	11.48 Å
Shape Rg shape_rg	11.18 Å
Total Rg total_rg	12.45 Å
Total atoms total_atoms	484
Residues n_residues	61
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	39.0 Å
Rg (real space) rg_real	12.19 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.2690e+06
I(0) uncertainty (real space) i0_real_error	1.3010e+04
Rg (reciprocal space) rg_reciprocal	12.19 Å
I(0) (reciprocal space) i0_reciprocal	1269000.0000
Solution quality estimate total_estimate	0.7523
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.3 Å
Skewness Skewness skewness	0.124
Kurtosis Kurtosis kurtosis	-0.427
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	151800.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 1.000; Smooth: 0.940

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b7da_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.7 — Scorpion toxin-like
Family Family family	g.3.7.1 — Long-chain scorpion toxins

CATH v4.4 (1 domains)

Domain ID domain_id	1b7dA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

▶

8. Citations (2)

▶

Unit-cell length a length_a	22.210 Å
Unit-cell length b length_b	36.540 Å
Unit-cell length c length_c	31.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	13.000 Å
R factor r_factor	—
R_work r_work	0.1780
R_free r_free	0.2380

Description description	PROTEIN (NEUROTOXIN TS1)
Molecular weight formula_weight	6901.0 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	553

NEUROTOXIN (TS1) FROM BRAZILIAN SCORPION TITYUS SERRULATUS

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

PROTEIN (NEUROTOXIN TS1)

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 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	65

fit	/app/data/saxs_computation/b7/1b7d/1b7d.fit
pddf	/app/data/pr_computation/b7/1b7d/1b7d.pr.out
profile	/app/data/saxs_computation/b7/1b7d/1b7d.dat