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- PDB-6zvm: Botulinum neurotoxin B2 binding domain in complex with GD1a -

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Basic information

Entry
Database: PDB / ID: 6zvm
TitleBotulinum neurotoxin B2 binding domain in complex with GD1a
ComponentsNeurotoxin
KeywordsTOXIN / botulinum neurotoxin / ganglioside / gd1a / bont / b2
Function / homology
Function and homology information


host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDavies, J.R. / Masuyer, G. / Stenmark, P.
CitationJournal: Toxins / Year: 2020
Title: Structural and Biochemical Characterization of Botulinum Neurotoxin Subtype B2 Binding to Its Receptors.
Authors: Davies, J.R. / Masuyer, G. / Stenmark, P.
History
DepositionJul 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9394
Polymers52,4651
Non-polymers1,4743
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint15 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.639, 56.162, 76.792
Angle α, β, γ (deg.)90.000, 121.996, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Neurotoxin / Neurotoxin B


Mass: 52464.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bontb / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8GR96
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...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


Type: oligosaccharide / Mass: 1290.140 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2-3/a4-b1_b3-c2_b4-d1_d3-e1_e3-f2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M calcium acetate hydrate, 0.08 M MES pH 6.5, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→63.816 Å / Num. obs: 46758 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.042 / Rrim(I) all: 0.109 / Χ2: 0.96 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2663 / CC1/2: 0.682 / Rpim(I) all: 0.356 / Rrim(I) all: 0.777 / Χ2: 1 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kbb

4kbb


Resolution: 1.8→63.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2032 2081 4.453 %
Rwork0.164 44653 -
all0.166 --
obs-46734 99.515 %
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.469 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å2-0.442 Å2
2--1.671 Å20 Å2
3----0.223 Å2
Refinement stepCycle: LAST / Resolution: 1.8→63.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 100 296 3998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133873
X-RAY DIFFRACTIONr_bond_other_d0.0350.0183430
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.6635243
X-RAY DIFFRACTIONr_angle_other_deg2.2621.5978008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4085.034444
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg123.144201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61423.636231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27915.022693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0191518
X-RAY DIFFRACTIONr_chiral_restr0.0640.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024278
X-RAY DIFFRACTIONr_gen_planes_other0.010.02853
X-RAY DIFFRACTIONr_nbd_refined0.1820.2583
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.23261
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21832
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1240.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.212
X-RAY DIFFRACTIONr_nbd_other0.2510.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2410.29
X-RAY DIFFRACTIONr_mcbond_it3.8941.9941742
X-RAY DIFFRACTIONr_mcbond_other3.8941.9941741
X-RAY DIFFRACTIONr_mcangle_it4.8232.9732188
X-RAY DIFFRACTIONr_mcangle_other4.8232.9732189
X-RAY DIFFRACTIONr_scbond_it6.2822.572128
X-RAY DIFFRACTIONr_scbond_other6.2812.572129
X-RAY DIFFRACTIONr_scangle_it8.7033.6353055
X-RAY DIFFRACTIONr_scangle_other8.7023.6353056
X-RAY DIFFRACTIONr_lrange_it9.95524.084374
X-RAY DIFFRACTIONr_lrange_other9.93523.8564320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2791540.2483146X-RAY DIFFRACTION96.1538
1.847-1.8970.231450.2163167X-RAY DIFFRACTION98.7772
1.897-1.9520.2441490.1973106X-RAY DIFFRACTION99.5109
1.952-2.0120.2311210.1913068X-RAY DIFFRACTION99.5629
2.012-2.0780.231380.1772962X-RAY DIFFRACTION99.7105
2.078-2.1510.2231250.1712839X-RAY DIFFRACTION99.9326
2.151-2.2320.2341040.1622746X-RAY DIFFRACTION99.7899
2.232-2.3230.2031530.1512629X-RAY DIFFRACTION99.8923
2.323-2.4260.1931660.152496X-RAY DIFFRACTION99.9624
2.426-2.5450.1941140.1532415X-RAY DIFFRACTION100
2.545-2.6820.2171120.162330X-RAY DIFFRACTION99.9591
2.682-2.8440.175930.1612201X-RAY DIFFRACTION99.9564
2.844-3.040.204970.1542053X-RAY DIFFRACTION100
3.04-3.2830.186800.161939X-RAY DIFFRACTION99.9505
3.283-3.5960.194640.1621784X-RAY DIFFRACTION100
3.596-4.0190.2610.1451635X-RAY DIFFRACTION100
4.019-4.6380.141570.1211426X-RAY DIFFRACTION100
4.638-5.6730.18750.1511208X-RAY DIFFRACTION100
5.673-7.9920.244460.206952X-RAY DIFFRACTION100
7.992-63.730.237270.2551X-RAY DIFFRACTION99.8273

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