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

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Basic information

Entry
Database: PDB / ID: 6xce
TitleStructure of the C. botulinum neurotoxin serotype A light chain protease in complex with covalent inhibitor 53
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
Chem-UZM / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.5Nov 6, 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)50,8202
Polymers50,4551
Non-polymers3651
Water99155
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 area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.062, 66.502, 65.107
Angle α, β, γ (deg.)90.000, 98.418, 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-UZM / (3S)-3-(2,4-dichlorophenyl)-N~1~-hydroxy-N~5~-(3-sulfanylpropyl)pentanediamide


Mass: 365.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18Cl2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
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: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54178 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→29.55 Å / Num. obs: 14436 / % possible obs: 95.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.05 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1233 / CC1/2: 0.74 / % possible all: 83.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BON

3bon


Resolution: 2.5→29.55 Å / SU ML: 0.3005 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9644 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3103 1417 10.01 %
Rwork0.2567 12737 -
obs0.2622 14154 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.63 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 22 55 3504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263530
X-RAY DIFFRACTIONf_angle_d0.54524776
X-RAY DIFFRACTIONf_chiral_restr0.0428519
X-RAY DIFFRACTIONf_plane_restr0.0037617
X-RAY DIFFRACTIONf_dihedral_angle_d8.08012094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.35631230.26981110X-RAY DIFFRACTION83.09
2.59-2.690.3261340.26281203X-RAY DIFFRACTION91.83
2.69-2.810.26711470.26471317X-RAY DIFFRACTION98.26
2.81-2.960.29221450.26731318X-RAY DIFFRACTION99.59
2.96-3.140.32731490.26641334X-RAY DIFFRACTION99.93
3.14-3.390.34931460.28961306X-RAY DIFFRACTION99.59
3.39-3.730.46071260.35221174X-RAY DIFFRACTION87.78
3.73-4.270.27611450.23841260X-RAY DIFFRACTION94.04
4.27-5.370.26031490.2011334X-RAY DIFFRACTION99.73
5.37-29.550.231530.20351381X-RAY DIFFRACTION99.93

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