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- PDB-5mk6: Crystal structure of the receptor-binding domain of botulinum neu... -

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Basic information

Entry
Database: PDB / ID: 5mk6
TitleCrystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal form 1)
ComponentsBotulinum neurotoxin type A
KeywordsTOXIN / bacterial / Toxin receptor binding domain / jelly roll fold / beta trefoil fold
Function / homology
Function and homology information


host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
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 ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsDavies, J.R. / Acharya, K.R.
CitationJournal: PeerJ / Year: 2018
Title: High resolution crystal structures of the receptor-binding domain ofClostridium botulinumneurotoxin serotypes A and FA.
Authors: Davies, J.R. / Hackett, G.S. / Liu, S.M. / Acharya, K.R.
History
DepositionDec 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7342
Polymers50,7111
Non-polymers231
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.770, 107.320, 107.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 50711.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Production host: Escherichia coli (E. coli)
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MIB, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.45→24.05 Å / Num. obs: 78738 / % possible obs: 95.9 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 6.9
Reflection shellResolution: 1.45→4.48 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.357 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.45→24.048 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.03
RfactorNum. reflection% reflection
Rfree0.2211 1985 2.52 %
Rwork0.1765 --
obs0.1776 78664 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→24.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 1 421 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023596
X-RAY DIFFRACTIONf_angle_d0.4424883
X-RAY DIFFRACTIONf_dihedral_angle_d13.8121357
X-RAY DIFFRACTIONf_chiral_restr0.07526
X-RAY DIFFRACTIONf_plane_restr0.002631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.38521330.31645441X-RAY DIFFRACTION95
1.4863-1.52650.29591540.2715495X-RAY DIFFRACTION97
1.5265-1.57140.26961590.24375486X-RAY DIFFRACTION97
1.5714-1.62210.29411600.23325444X-RAY DIFFRACTION97
1.6221-1.680.27041200.21915473X-RAY DIFFRACTION96
1.68-1.74730.26381600.19795531X-RAY DIFFRACTION97
1.7473-1.82680.24421370.18045541X-RAY DIFFRACTION97
1.8268-1.9230.24171530.17375490X-RAY DIFFRACTION97
1.923-2.04350.241520.16185392X-RAY DIFFRACTION94
2.0435-2.20120.23831390.15625491X-RAY DIFFRACTION95
2.2012-2.42250.19921260.16295490X-RAY DIFFRACTION96
2.4225-2.77260.21421290.17075474X-RAY DIFFRACTION94
2.7726-3.49140.20311320.16845457X-RAY DIFFRACTION93
3.4914-24.05080.16811310.15515474X-RAY DIFFRACTION90

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