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- PDB-7z5t: Crystal Structure of botulinum neurotoxin A2 cell binding domain -

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Basic information

Entry
Database: PDB / ID: 7z5t
TitleCrystal Structure of botulinum neurotoxin A2 cell binding domain
ComponentsBotulinum neurotoxin
KeywordsTOXIN / neurotoxin / botulinum / receptor / cell binding domain
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 / 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
ACETATE ION / Bontoxilysin-A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M. / Mahadeva, T.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Toxins / Year: 2022
Title: Structural Features of Clostridium botulinum Neurotoxin Subtype A2 Cell Binding Domain.
Authors: Gregory, K.S. / Mahadeva, T.B. / Liu, S.M. / Acharya, K.R.
History
DepositionMar 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Botulinum neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7143
Polymers50,4161
Non-polymers2972
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint0 kcal/mol
Surface area17810 Å2
Unit cell
Length a, b, c (Å)39.918, 100.786, 116.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Botulinum neurotoxin


Mass: 50416.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: A, bont / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4GGE0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1m Sodium acetate, 4.55% PEG 400, 4.55% PEG 500 MME, 4.55% PEG 600, 4.55% PEG 1000, 4.55% PEG 2000, 4.55% PEG 3350, 4.55% PEG 4000, 4.55% PEG 5000, 4.55% PEG 6000, 4.55% PEG 8000, 4.55% PEG 10000

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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: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.63→116.15 Å / Num. obs: 59567 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.031 / Net I/σ(I): 11.6
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 26.3 % / Rmerge(I) obs: 5.53 / Num. unique obs: 2930 / CC1/2: 0.299 / Rpim(I) all: 1.087 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MOY

5moy


Resolution: 1.63→76.123 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.186 / SU B: 2.952 / SU ML: 0.092 / Average fsc free: 0.8407 / Average fsc work: 0.857 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2367 2962 4.983 %
Rwork0.203 56484 -
all0.205 --
obs-59446 99.928 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.782 Å2
Baniso -1Baniso -2Baniso -3
1-1.613 Å2-0 Å20 Å2
2---0.806 Å2-0 Å2
3----0.807 Å2
Refinement stepCycle: LAST / Resolution: 1.63→76.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 20 214 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163306
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6334675
X-RAY DIFFRACTIONr_angle_other_deg1.3711.5897592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.815413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3424190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40715631
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg10.101151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0291515
X-RAY DIFFRACTIONr_chiral_restr0.0710.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
X-RAY DIFFRACTIONr_nbd_refined0.1920.2570
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.23152
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21652
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21788
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2188
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2970.26
X-RAY DIFFRACTIONr_nbd_other0.1490.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.213
X-RAY DIFFRACTIONr_mcbond_it2.612.9661644
X-RAY DIFFRACTIONr_mcbond_other2.6062.9631642
X-RAY DIFFRACTIONr_mcangle_it3.6244.4312053
X-RAY DIFFRACTIONr_mcangle_other3.6244.4342054
X-RAY DIFFRACTIONr_scbond_it3.6993.3921819
X-RAY DIFFRACTIONr_scbond_other3.6983.3931820
X-RAY DIFFRACTIONr_scangle_it5.4654.922620
X-RAY DIFFRACTIONr_scangle_other5.4644.9212621
X-RAY DIFFRACTIONr_lrange_it6.84734.3863820
X-RAY DIFFRACTIONr_lrange_other6.83334.2393794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.63-1.6720.3662180.34741420.34843630.510.54799.93120.345
1.672-1.7180.3552030.32840070.3342100.570.6151000.325
1.718-1.7680.3132140.29738900.29841040.7350.7571000.289
1.768-1.8220.2762120.26337980.26340130.8310.84999.92520.249
1.822-1.8820.2811790.24636870.24838670.860.86599.97410.227
1.882-1.9480.3321800.3135650.31137530.8050.81399.78680.288
1.948-2.0220.2561610.21334550.21536160.8980.9111000.189
2.022-2.1040.2321530.20133650.20335180.9260.9271000.177
2.104-2.1970.2441830.18931810.19233650.9220.93899.97030.165
2.197-2.3050.2841790.24830070.2532070.890.90999.34520.217
2.305-2.4290.2471590.18728960.1930550.9280.9441000.164
2.429-2.5760.2471500.18727720.1929220.9380.9491000.166
2.576-2.7540.2271430.19926000.227430.9280.941000.181
2.754-2.9740.2641300.19124380.19425680.9190.951000.175
2.974-3.2580.2151040.18922670.1923710.9430.9521000.18
3.258-3.6410.214940.19320660.19421630.9530.95599.86130.187
3.641-4.2030.2331020.17818120.18119150.9510.96299.94780.177
4.203-5.1440.1411020.14415510.14416530.9790.981000.147
5.144-7.2580.262640.17712410.18113050.9570.971000.18
7.258-76.1230.238320.2327430.2327770.9650.95999.74260.233

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