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- PDB-5mk7: Crystal structure of the receptor-binding domain of botulinum neu... -

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Basic information

Entry
Database: PDB / ID: 5mk7
TitleCrystal structure of the receptor-binding domain of botulinum neurotoxin A1 (crystal form 2)
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 / membrane => GO:0016020 / metalloendopeptidase activity / toxin activity ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / membrane => GO:0016020 / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
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 ...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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A


Theoretical massNumber of molelcules
Total (without water)50,7111
Polymers50,7111
Non-polymers00
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.363, 53.927, 62.687
Angle α, β, γ (deg.)90.00, 106.05, 90.00
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.42 %
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: Jun 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→60.5 Å / Num. obs: 36131 / % possible obs: 98.6 % / Redundancy: 20.4 % / CC1/2: 0.962 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 3.7 / CC1/2: 0.954 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VUA

2vua


Resolution: 1.8→60.242 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.28
RfactorNum. reflection% reflection
Rfree0.2231 1752 4.91 %
Rwork0.1876 --
obs0.1894 35708 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→60.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 0 322 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033331
X-RAY DIFFRACTIONf_angle_d0.6834504
X-RAY DIFFRACTIONf_dihedral_angle_d15.2991985
X-RAY DIFFRACTIONf_chiral_restr0.052482
X-RAY DIFFRACTIONf_plane_restr0.003576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84880.23511130.19042373X-RAY DIFFRACTION89
1.8488-1.90320.28231310.24582449X-RAY DIFFRACTION92
1.9032-1.96470.31011160.28022368X-RAY DIFFRACTION89
1.9647-2.03490.25391400.19182670X-RAY DIFFRACTION100
2.0349-2.11640.25061520.23112594X-RAY DIFFRACTION98
2.1164-2.21270.23821240.18532687X-RAY DIFFRACTION100
2.2127-2.32930.25441320.19932615X-RAY DIFFRACTION98
2.3293-2.47530.24641220.18892698X-RAY DIFFRACTION100
2.4753-2.66640.23451420.19722670X-RAY DIFFRACTION100
2.6664-2.93470.25171320.19162683X-RAY DIFFRACTION100
2.9347-3.35940.20231500.18072685X-RAY DIFFRACTION100
3.3594-4.23230.18461420.15992694X-RAY DIFFRACTION100
4.2323-60.2760.19631560.16652770X-RAY DIFFRACTION100

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