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- PDB-5vgv: Structure of the C. botulinum neurotoxin serotype A with Cu bound -

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Basic information

Entry
Database: PDB / ID: 5vgv
TitleStructure of the C. botulinum neurotoxin serotype A with Cu 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 / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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)RO1AI119564 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)50,7884
Polymers50,6021
Non-polymers1863
Water23413
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
MethodPISA
Unit cell
Length a, b, c (Å)49.626, 66.599, 65.548
Angle α, β, γ (deg.)90.00, 98.99, 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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#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.: 13 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000 6%, Calcium Acetate 0.1 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: 1.36994 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: 1.36994 Å / Relative weight: 1
ReflectionResolution: 2.6→31.965 Å / Num. obs: 12795 / % possible obs: 97 % / Redundancy: 7.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.1658 / Χ2: 1.508 / Net I/σ(I): 12.32
Reflection shellResolution: 2.6→2.693 Å / Redundancy: 5 % / Rmerge(I) obs: 0.3537 / Mean I/σ(I) obs: 3.92 / Num. unique obs: 1221 / CC1/2: 0.889 / Χ2: 0.679 / % possible all: 93

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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: 2.6→31.965 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2518 1290 10.05 %Random Selection/PHENIX Refine
Rwork0.2002 ---
obs0.2055 24230 95.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→31.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 6 13 3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033495
X-RAY DIFFRACTIONf_angle_d1.0574732
X-RAY DIFFRACTIONf_dihedral_angle_d12.9742080
X-RAY DIFFRACTIONf_chiral_restr0.043517
X-RAY DIFFRACTIONf_plane_restr0.011613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65310.34051370.25241195X-RAY DIFFRACTION89
2.6531-2.71070.31811290.27381154X-RAY DIFFRACTION87
2.7107-2.77370.3421430.26071289X-RAY DIFFRACTION94
2.7737-2.84310.34621420.26441285X-RAY DIFFRACTION96
2.8431-2.91990.35311450.25151331X-RAY DIFFRACTION96
2.9199-3.00570.34061380.24631236X-RAY DIFFRACTION94
3.0057-3.10270.32471500.22151326X-RAY DIFFRACTION98
3.1027-3.21350.2361420.23431302X-RAY DIFFRACTION98
3.2135-3.3420.29851530.21981362X-RAY DIFFRACTION97
3.342-3.49390.27371380.21161223X-RAY DIFFRACTION92
3.4939-3.67790.25861460.21051300X-RAY DIFFRACTION96
3.6779-3.90790.25181410.18781273X-RAY DIFFRACTION95
3.9079-4.20910.22551440.17331302X-RAY DIFFRACTION96
4.2091-4.63150.21411450.15651312X-RAY DIFFRACTION97
4.6315-5.2990.20121470.15751301X-RAY DIFFRACTION97
5.299-6.66630.24631500.1921315X-RAY DIFFRACTION97
6.6663-31.96780.16191440.16731290X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 15.1941 Å / Origin y: -0.5173 Å / Origin z: 16.1268 Å
111213212223313233
T0.0781 Å2-0.0236 Å2-0.0023 Å2-0.0989 Å2-0.0049 Å2--0.1076 Å2
L0.3834 °2-0.2793 °2-0.0364 °2-0.4555 °2-0.0274 °2--0.6523 °2
S0.0052 Å °0.0551 Å °-0.0325 Å °0.0377 Å °-0.0297 Å °0.0325 Å °-0.0041 Å °-0.0477 Å °-0.0011 Å °
Refinement TLS groupSelection details: all

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