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- PDB-6two: Binding domain of BoNT/A6 -

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Basic information

Entry
Database: PDB / ID: 6two
TitleBinding domain of BoNT/A6
ComponentsBont/A1
KeywordsTOXIN / binding domain / botulinum neurotoxin
Function / homology
Function and homology information


protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / 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: 1.35 Å
AuthorsDavies, J.R. / Britton, A. / Acharya, K.R.
CitationJournal: Febs Open Bio / Year: 2020
Title: High-resolution crystal structures of the botulinum neurotoxin binding domains from subtypes A5 and A6.
Authors: Davies, J.R. / Britton, A. / Liu, S.M. / Acharya, K.R.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7172
Polymers50,6821
Non-polymers351
Water8,755486
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area18870 Å2
Unit cell
Length a, b, c (Å)39.542, 105.587, 112.405
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 Bont/A1 / Botulinum neurotoxin type A


Mass: 50681.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C9WWY7
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Bis-Tris propane-HCl pH 7.5, 22% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.35→112.41 Å / Num. obs: 104434 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.999 / Net I/σ(I): 10.7
Reflection shellResolution: 1.35→1.37 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5129 / CC1/2: 0.463

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VUA

2vua


Resolution: 1.35→56.266 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.135 / SU B: 2.796 / SU ML: 0.047 / Average fsc free: 0.9388 / Average fsc work: 0.9432 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1776 2594 2.493 %
Rwork0.143 101438 -
all0.144 --
obs-104032 99.779 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.653 Å2
Baniso -1Baniso -2Baniso -3
1-2.757 Å20 Å20 Å2
2---1.398 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.35→56.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 1 486 3935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133737
X-RAY DIFFRACTIONr_bond_other_d0.0030.0173424
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.635089
X-RAY DIFFRACTIONr_angle_other_deg1.4951.5787990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8015472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37423.413208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50915692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8241520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024283
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02813
X-RAY DIFFRACTIONr_nbd_refined0.2220.2624
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23294
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21782
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21759
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2325
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.219
X-RAY DIFFRACTIONr_nbd_other0.2030.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3580.242
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1160.21
X-RAY DIFFRACTIONr_mcbond_it1.7321.8091792
X-RAY DIFFRACTIONr_mcbond_other1.7291.8071791
X-RAY DIFFRACTIONr_mcangle_it2.2952.7232278
X-RAY DIFFRACTIONr_mcangle_other2.2962.7252279
X-RAY DIFFRACTIONr_scbond_it2.0962.1361945
X-RAY DIFFRACTIONr_scbond_other2.0962.1371946
X-RAY DIFFRACTIONr_scangle_it2.683.0822805
X-RAY DIFFRACTIONr_scangle_other2.6793.0832806
X-RAY DIFFRACTIONr_lrange_it3.50622.5154317
X-RAY DIFFRACTIONr_lrange_other3.38121.954225
X-RAY DIFFRACTIONr_rigid_bond_restr5.01737161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.3151600.2977437X-RAY DIFFRACTION99.6197
1.385-1.4230.271740.2697213X-RAY DIFFRACTION99.4882
1.423-1.4640.2681730.2387041X-RAY DIFFRACTION99.5859
1.464-1.5090.2321860.2116805X-RAY DIFFRACTION99.6153
1.509-1.5590.2081840.1736588X-RAY DIFFRACTION99.6029
1.559-1.6130.1871860.1556366X-RAY DIFFRACTION99.726
1.613-1.6740.1681420.1356238X-RAY DIFFRACTION99.7498
1.674-1.7430.1611270.1225998X-RAY DIFFRACTION99.9021
1.743-1.820.1411260.1095764X-RAY DIFFRACTION99.8305
1.82-1.9090.1621590.1155478X-RAY DIFFRACTION99.8406
1.909-2.0120.1621320.1175244X-RAY DIFFRACTION99.9257
2.012-2.1340.191250.1154961X-RAY DIFFRACTION99.9018
2.134-2.2810.151360.1254678X-RAY DIFFRACTION99.9377
2.281-2.4640.1861130.1284378X-RAY DIFFRACTION99.9555
2.464-2.6990.1751040.1294043X-RAY DIFFRACTION99.9759
2.699-3.0170.158990.1393655X-RAY DIFFRACTION99.9734
3.017-3.4830.161040.1363255X-RAY DIFFRACTION100
3.483-4.2630.157780.1292781X-RAY DIFFRACTION100
4.263-6.020.181610.1442201X-RAY DIFFRACTION100
6.02-56.2660.271250.1971314X-RAY DIFFRACTION99.7765

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