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- PDB-5vgx: Structure of the C. botulinum neurotoxin serotype A with Hg bound -

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Basic information

Entry
Database: PDB / ID: 5vgx
TitleStructure of the C. botulinum neurotoxin serotype A with Hg bound
ComponentsBotulinum neurotoxin type A
KeywordsTOXIN / botulinum / neurotoxin / metalloprotease
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
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCarolan, J.P. / 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. Am. Chem. Soc. / Year: 2017
Title: Metal Ions Effectively Ablate the Action of Botulinum Neurotoxin A.
Authors: Bremer, P.T. / Pellett, S. / Carolan, J.P. / Tepp, W.H. / Eubanks, L.M. / Allen, K.N. / Johnson, E.A. / Janda, K.D.
History
DepositionApr 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8623
Polymers50,6021
Non-polymers2602
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Identity confirmed by genetic sequencing, denaturing electrophoresis, and enzymatic activity assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-27 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.449, 66.677, 65.115
Angle α, β, γ (deg.)90.00, 98.92, 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: 50602.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Polyhistidine-tagged botulinum neurotoxin A light chain
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000 8%, Calcium Acetate 0.2 M, Sodium Cacodylate 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 Stream
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.99164 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2017 / Details: Mirror: Rh coated flat, toroidal focusing
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99164 Å / Relative weight: 1
ReflectionResolution: 2.15→27.5393 Å / Num. obs: 22337 / % possible obs: 98 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.46 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.1515 / Χ2: 1.084 / Net I/σ(I): 8.11
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.3144 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2145 / CC1/2: 0.909 / Χ2: 0.371 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BOK

3bok


Resolution: 2.15→27.537 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.81
Details: Refinement performed utilizing XYZ coordinate, real space, TLS, anomalous groups, and individual B-factor parameters.
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 2477 5.83 %Random Selection/PHENIX Refine
Rwork0.1955 ---
obs0.1984 22328 95.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→27.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 5 98 3511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033491
X-RAY DIFFRACTIONf_angle_d0.5144725
X-RAY DIFFRACTIONf_dihedral_angle_d15.8542075
X-RAY DIFFRACTIONf_chiral_restr0.042516
X-RAY DIFFRACTIONf_plane_restr0.005612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.19130.30661260.23142084X-RAY DIFFRACTION90
2.1913-2.23610.28771380.21362187X-RAY DIFFRACTION92
2.2361-2.28470.26691330.21022186X-RAY DIFFRACTION94
2.2847-2.33780.2581380.21742218X-RAY DIFFRACTION94
2.3378-2.39620.27241390.22152183X-RAY DIFFRACTION94
2.3962-2.4610.30561300.22322068X-RAY DIFFRACTION89
2.461-2.53330.30851380.21582273X-RAY DIFFRACTION98
2.5333-2.6150.27451440.20912324X-RAY DIFFRACTION99
2.615-2.70840.30851430.2182304X-RAY DIFFRACTION98
2.7084-2.81680.29181410.22652290X-RAY DIFFRACTION98
2.8168-2.94480.31311380.22572255X-RAY DIFFRACTION97
2.9448-3.09990.29921390.22182241X-RAY DIFFRACTION95
3.0999-3.29380.25331340.21252181X-RAY DIFFRACTION94
3.2938-3.54760.24861420.18912295X-RAY DIFFRACTION98
3.5476-3.90370.19751410.17132270X-RAY DIFFRACTION98
3.9037-4.46650.19971400.15212235X-RAY DIFFRACTION95
4.4665-5.61950.18561360.16482171X-RAY DIFFRACTION94
5.6195-27.53930.19681370.18352237X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 5.1333 Å / Origin y: -0.583 Å / Origin z: 80.5388 Å
111213212223313233
T0.2359 Å2-0.0329 Å2-0.0269 Å2-0.1384 Å20.0039 Å2--0.1485 Å2
L1.0926 °2-0.5579 °2-0.338 °2-1.1085 °20.3151 °2--1.3802 °2
S0.0705 Å °0.0912 Å °-0.0082 Å °-0.0648 Å °-0.0686 Å °0.1076 Å °-0.0832 Å °-0.1195 Å °0.0005 Å °
Refinement TLS groupSelection details: all

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