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- PDB-6xcc: Structure of the C. botulinum neurotoxin serotype A light chain p... -

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Basic information

Entry
Database: PDB / ID: 6xcc
TitleStructure of the C. botulinum neurotoxin serotype A light chain protease in complex with covalent inhibitor 21
ComponentsBotulinum neurotoxin type A
KeywordsTOXIN/INHIBITOR / covalent inhibitor / hydroxamate / TOXIN / TOXIN-INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated suppression of host exocytosis / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity ...symbiont-mediated suppression of host exocytosis / ganglioside GT1b binding / Toxicity of botulinum toxin type A (botA) / bontoxilysin / 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 / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
N-hydroxy-5-sulfanylpentanamide / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTararina, M.A. / Allen, K.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI119564 United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Catch and Anchor Approach To Combat Both Toxicity and Longevity of Botulinum Toxin A.
Authors: Lin, L. / Olson, M.E. / Sugane, T. / Turner, L.D. / Tararina, M.A. / Nielsen, A.L. / Kurbanov, E.K. / Pellett, S. / Johnson, E.A. / Cohen, S.M. / Allen, K.N. / Janda, K.D.
History
DepositionJun 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jun 9, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 18, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)50,6693
Polymers50,4551
Non-polymers2152
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.411, 66.692, 64.909
Angle α, β, γ (deg.)90.000, 98.588, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX / Botulinum neurotoxin type A1


Mass: 50454.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bonT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0DPI0, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UZV / N-hydroxy-5-sulfanylpentanamide


Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.3 - 0.45 M ammonium tartrate dibasic, 15 - 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91989 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91989 Å / Relative weight: 1
ReflectionResolution: 1.9→29.59 Å / Num. obs: 32771 / % possible obs: 96.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.44 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1949 / CC1/2: 0.695

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BON

3bon


Resolution: 1.9→29.59 Å / SU ML: 0.2594 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.1047 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2348 1999 6.11 %
Rwork0.1891 30723 -
obs0.1919 32722 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 10 211 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683524
X-RAY DIFFRACTIONf_angle_d0.8254767
X-RAY DIFFRACTIONf_chiral_restr0.0548519
X-RAY DIFFRACTIONf_plane_restr0.0052617
X-RAY DIFFRACTIONf_dihedral_angle_d5.54812928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.39721140.34781724X-RAY DIFFRACTION76.08
1.94-20.35771430.29812199X-RAY DIFFRACTION98.16
2-2.050.29641430.26542193X-RAY DIFFRACTION98.11
2.05-2.120.2941430.25262218X-RAY DIFFRACTION97.76
2.12-2.20.27841450.232231X-RAY DIFFRACTION97.82
2.2-2.280.28541430.21092204X-RAY DIFFRACTION97.95
2.28-2.390.24131460.20382230X-RAY DIFFRACTION98.34
2.39-2.510.2621450.20342244X-RAY DIFFRACTION98.76
2.51-2.670.25721450.19152215X-RAY DIFFRACTION98.54
2.67-2.880.23451440.19322234X-RAY DIFFRACTION98.8
2.88-3.170.24321470.19622249X-RAY DIFFRACTION98.48
3.17-3.620.24921460.17722241X-RAY DIFFRACTION98.35
3.62-4.560.18491450.15392235X-RAY DIFFRACTION97.66
4.56-29.590.19281500.16262306X-RAY DIFFRACTION98.87

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