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

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Basic information

Entry
Database: PDB / ID: 6xcf
TitleStructure of the C. botulinum neurotoxin serotype A light chain protease in complex with noncovalent inhibitor 59
ComponentsBotulinum neurotoxin type A
KeywordsTOXIN/INHIBITOR / covalent inhibitor / hydroxamate / TOXIN / TOXIN-INHIBITOR complex
Function / homology
Function and homology information


Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane ...Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / 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 / 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 C-terminal / Clostridium neurotoxin, receptor binding N-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 C-terminal / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / 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-UZP / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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
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)50,8823
Polymers50,4551
Non-polymers4272
Water5,368298
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 area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.339, 66.245, 64.057
Angle α, β, γ (deg.)90.000, 98.524, 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-UZP / (3R)-3-(2,4-dichlorophenyl)-N~1~-hydroxy-N~5~-pentylpentanediamide


Mass: 361.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22Cl2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 40.06 %
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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.68→39.29 Å / Num. obs: 45292 / % possible obs: 96.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.1
Reflection shellResolution: 1.68→1.7 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1410 / CC1/2: 0.785 / % possible all: 58.2

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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: 1.68→39.29 Å / SU ML: 0.1595 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3866 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1993 1998 4.42 %
Rwork0.1591 43195 -
obs0.1608 45193 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.98 Å2
Refinement stepCycle: LAST / Resolution: 1.68→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 24 298 3699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01643479
X-RAY DIFFRACTIONf_angle_d1.27624705
X-RAY DIFFRACTIONf_chiral_restr0.084512
X-RAY DIFFRACTIONf_plane_restr0.009606
X-RAY DIFFRACTIONf_dihedral_angle_d8.45412063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.2876980.28012140X-RAY DIFFRACTION66.99
1.72-1.760.29791430.23823088X-RAY DIFFRACTION96.3
1.76-1.820.27361450.20973143X-RAY DIFFRACTION98.92
1.82-1.870.20911470.18943159X-RAY DIFFRACTION98.86
1.87-1.940.26731440.18733103X-RAY DIFFRACTION97.71
1.94-2.020.23541440.16913120X-RAY DIFFRACTION96.91
2.02-2.110.19731460.16463152X-RAY DIFFRACTION98.89
2.11-2.220.20321470.15043195X-RAY DIFFRACTION99.17
2.22-2.360.20961460.15693143X-RAY DIFFRACTION97.83
2.36-2.540.20551450.15763125X-RAY DIFFRACTION98.49
2.54-2.80.22311470.16613185X-RAY DIFFRACTION98.96
2.8-3.20.1781480.15583181X-RAY DIFFRACTION98.46
3.2-4.040.16621480.13733202X-RAY DIFFRACTION99.2
4.04-39.290.18011500.14633259X-RAY DIFFRACTION99.01
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7109614623710.2778666767760.2342518287321.45428878509-0.2902677500182.06959354014-0.009437909232920.0804856314947-0.0317278859351-0.210825369848-0.0279882380885-0.1916139868950.06506438119810.2254225719790.01356600849550.2035438258220.023822656980.01843230746950.1356590860610.006764868952870.1468409313435.11093502819-0.5537394884044.84644938348
20.8058762798450.476885823220.09680487001591.18532539725-0.3504605705411.06751426554-0.00585069970413-0.0523937685394-0.0952049455804-0.00155869313424-0.0832400502912-0.1705218852520.08634343672070.1956674605590.09411898697380.2018236781240.03258240326780.0003859150305020.1577910013120.01019921037380.1815981497057.11770525908-4.9128921914918.8562235232
31.130677129010.6538079010350.09573941591141.43883969097-0.2604377593131.1435417221-0.0104079829456-0.08484524356710.05779600117750.0990381545452-0.0446398971318-0.0484089763363-0.1583211218550.05148295035910.04990262800510.2404508373970.0338464474722-0.01395384184840.151421079924-0.006145839045490.1538962366182.916418042733.684060387121.9546969917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 422 )

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