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6zvm

Botulinum neurotoxin B2 binding domain in complex with GD1a

Method: X-RAY DIFFRACTION Dmax: 82.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurotoxin

Clostridium botulinum

UniProt Q8GR96

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 AAA； UniProt 857–1291 Not recorded ;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-(1-4)-beta-D-glucopyranose ; × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.16 M calcium acetate hydrate, 0.08 M MES pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol Resolution 1.80 Å R-free 0.203

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 6ZVM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6ZVN Botulinum neurotoxin B2 binding domain in complex with human synaptotagmin I Deposited 2020-07-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain AAA 857–1291（435 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.1 M imidazole pH 8.0, 10% (w/v) PEG 8000
Resolution 2.50 Å R-free 0.283

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

View Construct and Data Evidence
UniProt name Q8GR96_CLOBO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain AAA； PDBConstruct 4–438； UniProt 857–1291

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 6zvm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zvm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6zvm
Deposition date deposition_date2020-07-25
Structure title titleBotulinum neurotoxin B2 binding domain in complex with GD1a
Keywords keywordsbotulinum neurotoxin, ganglioside, gd1a, bont, b2, 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_guinier25.46 Å
Radius of gyration Rg (electron density) rg_electron24.35 Å
Forward intensity I(0) i043883600.00
Molecular weight molecular_weight52332.0 kDa
Excluded volume excluded_volume65839 ų
Envelope volume envelope_volume77964 ų
Hydration-shell volume shell_volume26900 ų
Envelope diameter envelope_diameter85.2 Å
Shell Rg shell_rg31.46 Å
Envelope Rg envelope_rg24.65 Å
Shape Rg shape_rg24.32 Å
Total Rg total_rg25.29 Å
Total atoms total_atoms3702
Residues n_residues425
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 dmax82.8 Å
Rg (real space) rg_real25.48 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real4.3880e+07
I(0) uncertainty (real space) i0_real_error6.2990e+05
Rg (reciprocal space) rg_reciprocal25.47 Å
I(0) (reciprocal space) i0_reciprocal43880000.0000
Solution quality estimate total_estimate0.8920
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.0 Å
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.351
Angular range angular_range— – 0.3100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9220000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.975
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)