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4fvv

Crystal structure of HCR/D-Sa-GBL1/C

Method: X-RAY DIFFRACTION Dmax: 102.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurotoxin

Clostridium botulinum

UniProt Q9LBR1

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 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 862–1285 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

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 4FVV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3N7L Crystal structure of botulinum neurotoxin serotype D/C VPI 5993 binding domain Deposited 2010-05-27 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)
Not recorded 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
3N7M Crystal structure of W1252A mutant of HCR D/C VPI 5995 Deposited 2010-05-27 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：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
4ISQ Binding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I Deposited 2013-01-17 Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 8 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 1–423； UniProt 862–1285 Author chain B； PDBConstruct 1–423； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 4fvv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fvv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fvv
Deposition date deposition_date2012-06-29
Structure title titleCrystal structure of HCR/D-Sa-GBL1/C
Keywords keywordsbotulinum toxin, ganglioside bing loop, Ganglioside, TOXIN; TOXIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.12 Å
Radius of gyration Rg (electron density) rg_electron31.18 Å
Forward intensity I(0) i0142795000.00
Molecular weight molecular_weight96367.0 kDa
Excluded volume excluded_volume121040 ų
Envelope volume envelope_volume150040 ų
Hydration-shell volume shell_volume39949 ų
Envelope diameter envelope_diameter106.1 Å
Shell Rg shell_rg38.23 Å
Envelope Rg envelope_rg30.93 Å
Shape Rg shape_rg31.13 Å
Total Rg total_rg31.94 Å
Total atoms total_atoms6795
Residues n_residues827
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax102.7 Å
Rg (real space) rg_real32.00 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real1.4280e+08
I(0) uncertainty (real space) i0_real_error2.6050e+06
Rg (reciprocal space) rg_reciprocal32.06 Å
I(0) (reciprocal space) i0_reciprocal142800000.0000
Solution quality estimate total_estimate0.8962
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.9 Å
Skewness Skewness skewness0.199
Kurtosis Kurtosis kurtosis-0.497
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57500000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.902
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4fvva1
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.0 — automated matches
Domain ID domain_idd4fvva2
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.4 — STI-like
Family Family familyb.42.4.0 — automated matches
Domain ID domain_idd4fvvb1
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.0 — automated matches
Domain ID domain_idd4fvvb2
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.4 — STI-like
Family Family familyb.42.4.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id4fvvA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id4fvvA02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id4fvvB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id4fvvB02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
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8. Citations (1)

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9. Files and Curves (10)