SAXSdb — 1djt

▼

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

ALPHA-LIKE NEUROTOXIN BMK M1

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 15–78 Chain B； UniProt 15–78	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；2.8M NAH2PO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.20 Å

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 1DJT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SN1 STRUCTURE OF SCORPION NEUROTOXIN BMK M1 Deposited 1998-11-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–83（64 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.70 Å R-free 0.209
1T7A Crystal structure of mutant Lys8Asp of scorpion alpha-like neurotoxin BmK M1 from Buthus martensii Karsch Deposited 2004-05-08	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–83（64 aa）	Mutation：K8D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.183
1T7B Crystal structure of mutant Lys8Gln of scorpion alpha-like neurotoxin BmK M1 from Buthus martensii Karsch Deposited 2004-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–83（64 aa）	Mutation：K8Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, sodium cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.196
1T7E Crystal structure of mutant Pro9Ser of scorpion alpha-like neurotoxin BmK M1 from Buthus martensii Karsch Deposited 2004-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–83（64 aa）	Mutation：P9S	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；Sodium phosphate, PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.216
1ZU3 Crystal Structure Of Mutant K8A Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch Deposited 2005-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–83（65 aa）	Mutation：K8A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；30% (w/v) PEG8000, 0.1M sodium cacodylate pH 6.5, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.33 Å R-free 0.190
1ZUT Crystal Structure Of Mutant K8DP9SR58K Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch Deposited 2005-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–83（65 aa）	Mutation：K10D, P11S, R60K	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；30% (w/v) PEG8000, 0.1M sodium cacodylate pH 6.5, 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.229
1ZVE Crystal Structure Of Mutant K8G Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch Deposited 2005-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–83（65 aa）	Mutation：K10G	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% (w/v) PEG4000, 0.1 M Tris-HCl at pH 8.5, 0.2 M sodium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.223
1ZVG Crystal Structure Of Mutant K8DP9S Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch Deposited 2005-06-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–83（65 aa）	Mutation：K10D, P11S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.5M sodium phosphates, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.162
1ZYV Crystal Structure Of Mutant K8DP9SR58KV59G Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch Deposited 2005-06-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–83（65 aa）	Mutation：K10D, P11S, R60K, V61G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；30% (w/v) PEG4000, 0.1M Tris-HCl pH 8.5, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.198
1ZYW Crystal Structure Of Mutant K8DP9SR58KP60G Of Scorpion alpha-Like Neurotoxin Bmk M1 From Buthus Martensii Karsch Deposited 2005-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–83（65 aa）	Mutation：K10D, P11S, R60K, P62G	SO4 SULFATE ION × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；30% (w/v) PEG8000, 0.1M sodium cacodylate pH 6.5, 0.2M ammonium sulfate, 0.02M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.30 Å R-free 0.171

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SCX1_MESMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–64； UniProt 15–78 Author chain B； PDBConstruct 1–64； UniProt 15–78

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	1djt
Deposition date deposition_date	1999-12-05
Structure title title	ATOMIC RESOLUTION STRUCTURE OF SCORPION ALPHA-LIKE TOXIN BMK M1 IN A NEW CRYSTAL FORM
Keywords keywords	SCORPION, ALPHA-LIKE NEUROTOXIN, NON-PROLINE CIS PEPTIDE BOND, ATOMIC RESOLUTION, 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	15.06 Å
Radius of gyration Rg (electron density) rg_electron	14.39 Å
Forward intensity I(0) i0	4642680.00
Molecular weight molecular_weight	14455.0 kDa
Excluded volume excluded_volume	17643 Å³
Envelope volume envelope_volume	19599 Å³
Hydration-shell volume shell_volume	11819 Å³
Envelope diameter envelope_diameter	48.8 Å
Shell Rg shell_rg	19.66 Å
Envelope Rg envelope_rg	14.59 Å
Shape Rg shape_rg	14.42 Å
Total Rg total_rg	15.29 Å
Total atoms total_atoms	1006
Residues n_residues	128
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	50.5 Å
Rg (real space) rg_real	14.99 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	4.6430e+06
I(0) uncertainty (real space) i0_real_error	4.3500e+04
Rg (reciprocal space) rg_reciprocal	15.00 Å
I(0) (reciprocal space) i0_reciprocal	4643000.0000
Solution quality estimate total_estimate	0.8839
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.5 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.326
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	563300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.995

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1djta_
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

Domain ID domain_id	d1djtb_
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 (2 domains)

Domain ID domain_id	1djtA00
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

Domain ID domain_id	1djtB00
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	27.120 Å
Unit-cell length b length_b	52.770 Å
Unit-cell length c length_c	76.390 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1090
R_work r_work	—
R_free r_free	—

Description description	ALPHA-LIKE NEUROTOXIN BMK M1
Molecular weight formula_weight	7235.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1213

ATOMIC RESOLUTION STRUCTURE OF SCORPION ALPHA-LIKE TOXIN BMK M1 IN A NEW CRYSTAL FORM

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

ALPHA-LIKE NEUROTOXIN BMK M1

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

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

fit	/app/data/saxs_computation/dj/1djt/1djt.fit
pddf	/app/data/pr_computation/dj/1djt/1djt.pr.out
profile	/app/data/saxs_computation/dj/1djt/1djt.dat