SAXSdb — 3n7l

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

Neurotoxin

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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 862–1285	Fragment：Receptor Binding Domain (UNP residues 862-1285)	SO4 SULFATE ION × 3 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；292 K；0.1M MES pH 6.0, 5% PEG400, 1.8 M ammonium, 250 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.00 Å R-free 0.257

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 3N7L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3N7M Crystal structure of W1252A mutant of HCR D/C VPI 5995 Deposited 2010-05-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 862–1285（424 aa） Fragment：Receptor Binding Domain (UNP residues 862-1285)	Mutation：W1252A	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1M Hepes pH 7.5, 4% PEG400, 45% ammonium sulfate, 250mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.60 Å R-free 0.270
4FVV Crystal structure of HCR/D-Sa-GBL1/C Deposited 2012-06-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 862–1285（424 aa） Fragment：receptor binding domain, UNP residues 862-1285	Mutation：loop of KLGDDYWFN(1246-1254) mutated to RLGGDWYR	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；292 K；16% PEG5K-MME, 50 mM MgSO4, 0.1 M HEPPs buffer, pH 8.5, EVAPORATION, temperature 292K	Resolution 2.70 Å R-free 0.263
4FVV Crystal structure of HCR/D-Sa-GBL1/C Deposited 2012-06-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 862–1285（424 aa） Fragment：receptor binding domain, UNP residues 862-1285	Mutation：loop of KLGDDYWFN(1246-1254) mutated to RLGGDWYR	GOL GLYCEROL × 2 SIA N-acetyl-alpha-neuraminic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；292 K；16% PEG5K-MME, 50 mM MgSO4, 0.1 M HEPPs buffer, pH 8.5, EVAPORATION, temperature 292K	Resolution 2.70 Å R-free 0.263
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17	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 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.65 Å R-free 0.220
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17	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 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.65 Å R-free 0.220
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 8 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.65 Å R-free 0.220
4ISR Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II Deposited 2013-01-17	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 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.59 Å R-free 0.235
4ISR Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II Deposited 2013-01-17	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 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.59 Å R-free 0.235
4ISR Binding domain of Botulinum neurotoxin DC in complex with rat synaptotagmin II Deposited 2013-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 864–1285（422 aa） Fragment：Hc domain (unp residues 864-1285)	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.59 Å R-free 0.235

4 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9LBR1_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–424； UniProt 862–1285

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	3n7l
Deposition date deposition_date	2010-05-27
Structure title title	Crystal structure of botulinum neurotoxin serotype D/C VPI 5993 binding domain
Keywords keywords	Botulinum neurotoxin, HCR/D-SA, Ganglioside Binding Loop, 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	25.82 Å
Radius of gyration Rg (electron density) rg_electron	24.83 Å
Forward intensity I(0) i0	39524200.00
Molecular weight molecular_weight	49172.0 kDa
Excluded volume excluded_volume	61733 Å³
Envelope volume envelope_volume	73184 Å³
Hydration-shell volume shell_volume	25350 Å³
Envelope diameter envelope_diameter	93.0 Å
Shell Rg shell_rg	31.23 Å
Envelope Rg envelope_rg	25.15 Å
Shape Rg shape_rg	24.78 Å
Total Rg total_rg	25.72 Å
Total atoms total_atoms	3463
Residues n_residues	418
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	87.8 Å
Rg (real space) rg_real	25.91 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	3.9520e+07
I(0) uncertainty (real space) i0_real_error	5.8510e+05
Rg (reciprocal space) rg_reciprocal	25.89 Å
I(0) (reciprocal space) i0_reciprocal	39520000.0000
Solution quality estimate total_estimate	0.8584
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.3 Å
Skewness Skewness skewness	0.473
Kurtosis Kurtosis kurtosis	-0.310
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8078000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Neurotoxin
Molecular weight formula_weight	49038.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3632

NSINDSKILSLQNKKNTLMDTSGYNAEVRVEGNVQLNPIFPFDFKLGSSGDDRGKVIVTQNENIVYNAMYESFSISFWIRINKWVSNLPGYTIIDSVKNNSGWSIGIISNFLVFTLKQNENSEQDINFSYDISKNAAGYNKWFFVTITTNMMGNMMIYINGKLIDTIKVKELTGINFSKTITFQMNKIPNTGLITSDSDNINMWIRDFYIFAKELDDKDINILFNSLQYTNVVKDYWGNDLRYDKEYYMINVNYMNRYMSKKGNGIVFNTRKNNNDFNEGYKIIIKRIRGNTNDTRVRGENVLYFNTTIDNKQYSLGMYKPSRNLGTDLVPLGALDQPMDEIRKYGSFIIQPCNTFDYYASQLFLSSNATTNRLGILSIGSYSFKLGDDYWFNHEYLIPVIKIEHYASLLESTSTHWVFVPASE

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3n7la1
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	d3n7la2
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 (2 domains)

Domain ID domain_id	3n7lA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3n7lA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	57.294 Å
Unit-cell length b length_b	57.810 Å
Unit-cell length c length_c	184.191 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	28.910 Å
R factor r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2570

fit	/app/data/saxs_computation/n7/3n7l/3n7l.fit
pddf	/app/data/pr_computation/n7/3n7l/3n7l.pr.out
profile	/app/data/saxs_computation/n7/3n7l/3n7l.dat

Crystal structure of botulinum neurotoxin serotype D/C VPI 5993 binding domain

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

Neurotoxin

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