SAXSdb — 3rsj

▼

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

BoNT/F

Clostridium botulinum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 866–1278	Fragment：Receptor Binding Domain (UNP Residues 866-1276)	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	Resolution 2.00 Å R-free 0.263
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 866–1278	Fragment：Receptor Binding Domain (UNP Residues 866-1276)	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	Resolution 2.00 Å R-free 0.263
3	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 866–1278	Fragment：Receptor Binding Domain (UNP Residues 866-1276)	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	Resolution 2.00 Å R-free 0.263
4	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 866–1278	Fragment：Receptor Binding Domain (UNP Residues 866-1276)	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；292 K；0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K	Resolution 2.00 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.

Other PDB	Difference from Current Entry 3RSJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FIE Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1) Deposited 2008-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–419（419 aa） Fragment：residues 1-419, catalytic domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.279
3FIE Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1) Deposited 2008-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–419（419 aa） Fragment：residues 1-419, catalytic domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.10 Å R-free 0.279
3FII Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh2) Deposited 2008-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–419（419 aa） Fragment：residues 1-419, catalytic domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；298 K；0.1M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.17 Å R-free 0.290
3FUQ Glycosylated SV2 and Gangliosides as Dual Receptors for Botulinum Neurotoxin Serotype F Deposited 2009-01-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 862–1278（417 aa） Fragment：sequence database residues 862-1278	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；0.1 M Tris-HCL, 18% ethanol and 150 mM NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.10 Å R-free 0.243

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q57236_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–413； UniProt 866–1278 Author chain B； PDBConstruct 1–413； UniProt 866–1278 Author chain C； PDBConstruct 1–413； UniProt 866–1278 Author chain D； PDBConstruct 1–413； UniProt 866–1278

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	3rsj
Deposition date deposition_date	2011-05-02
Structure title title	Structure of HCRF in complex with Ganglioside GD1a
Keywords keywords	clostridium botulinum type F, ganglioside binding site, GD1a, 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	40.50 Å
Radius of gyration Rg (electron density) rg_electron	39.80 Å
Forward intensity I(0) i0	550407000.00
Molecular weight molecular_weight	191080.0 kDa
Excluded volume excluded_volume	238680 Å³
Envelope volume envelope_volume	304210 Å³
Hydration-shell volume shell_volume	63659 Å³
Envelope diameter envelope_diameter	145.4 Å
Shell Rg shell_rg	45.26 Å
Envelope Rg envelope_rg	39.33 Å
Shape Rg shape_rg	39.78 Å
Total Rg total_rg	40.15 Å
Total atoms total_atoms	13498
Residues n_residues	1614
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	133.8 Å
Rg (real space) rg_real	40.51 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	5.5040e+08
I(0) uncertainty (real space) i0_real_error	9.7500e+06
Rg (reciprocal space) rg_reciprocal	40.50 Å
I(0) (reciprocal space) i0_reciprocal	550400000.0000
Solution quality estimate total_estimate	0.8648
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.0 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.150
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	89680000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.683

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	BoNT/F
Molecular weight formula_weight	47912.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13922

IKDNSILDMRYENNKFIDISGYGSNISINGDVYIYSTNRNQFGIYSSKPSEVNIAQNNDIIYNGRYQNFSISFWVRIPKYFNKVNLNNEYTIIDCIRNNNSGWKISLNYNKIIWTLQDTAGNNQKLVFNYTQMISISDYINKWIFVTITNNRLGNSRIYINGNLIDEKSISNLGDIHVSDNILFKIVGCNDTRYVGIRYFKVFDTELGKTEIETLYSDEPDPSILKDFWGNYLLYNKRYYLLNLLRTDKSITQNSNFLNINQQRGVYQKPNIFSNTRLYTGVEVIIRKNGSTDISNTDNFVRKNDLAYINVVDRDVEYRLYADISIAKPEKIIKLIRTSNSNNSLGQIIVMDSIGNNCTMNFQNNNGGNIGLLGFHSNNLVASSWYYNNIRKNTSSNGCFWSFISKEHGWQEN

来源 Source

来源生物 organism	Clostridium botulinum
NCBI Class编号 ncbi_taxonomy_id	1491
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose
Molecular weight formula_weight	674.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose ;
Molecular weight formula_weight	1128.0 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose ;
Molecular weight formula_weight	836.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	424

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3rsja1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3rsja2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.0 — automated matches

Domain ID domain_id	d3rsjb1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3rsjb2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.0 — automated matches

Domain ID domain_id	d3rsjc1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3rsjc2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.0 — automated matches

Domain ID domain_id	d3rsjd1
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3rsjd2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3rsjA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3rsjA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3rsjB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3rsjB02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3rsjC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3rsjC02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3rsjD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3rsjD02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	65.468 Å
Unit-cell length b length_b	84.266 Å
Unit-cell length c length_c	117.600 Å
Unit-cell angle α angle_alpha	72.55 °
Unit-cell angle β angle_beta	87.01 °
Unit-cell angle γ angle_gamma	67.13 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.860 Å
R factor r_factor	0.2320
R_work r_work	0.2320
R_free r_free	0.2630

fit	/app/data/saxs_computation/rs/3rsj/3rsj.fit
pddf	/app/data/pr_computation/rs/3rsj/3rsj.pr.out
profile	/app/data/saxs_computation/rs/3rsj/3rsj.dat

Structure of HCRF in complex with Ganglioside GD1a

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

BoNT/F

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