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- PDB-3nf3: Crystal structure of BoNT/A LC with JTH-NB-7239 peptide -

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Basic information

Entry
Database: PDB / ID: 3nf3
TitleCrystal structure of BoNT/A LC with JTH-NB-7239 peptide
Components
  • BoNT/A
  • JTH-NB72-39 inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Botulinum neurotoxin / SNARE / BOTULISM / INHIBITION / METALLOPROTEASE / NEUROTRANSMISSION / NEUROMUSCULAR JUNCTION / HYDROLASE / MEMBRANE / METAL-BINDING / PROTEASE / SECRETED / TOXIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
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 / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
JTH-NB72-39 / NICKEL (II) ION / BoNT/A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZuniga, J.E.
CitationJournal: Plos One / Year: 2010
Title: Iterative structure-based peptide-like inhibitor design against the botulinum neurotoxin serotype A.
Authors: Zuniga, J.E. / Hammill, J.T. / Drory, O. / Nuss, J.E. / Burnett, J.C. / Gussio, R. / Wipf, P. / Bavari, S. / Brunger, A.T.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BoNT/A
C: JTH-NB72-39 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7794
Polymers49,6552
Non-polymers1242
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-4 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.100, 189.600, 41.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BoNT/A / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT


Mass: 48704.070 Da / Num. of mol.: 1 / Fragment: Light Chain, residues 1-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont/a, boNT/A, bonta / Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8V4
#2: Protein/peptide JTH-NB72-39 inhibitor


Type: Peptide-like / Class: Inhibitor / Mass: 951.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: JTH-NB72-39
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / pH: 7.4
Details: 14% PEG MME 2000, 10mM NiCl2, 100mM HEPES pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 6, 2009
RadiationMonochromator: SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. obs: 16177 / % possible obs: 88.9 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DSE

3dse


Resolution: 2.4→38.02 Å / SU ML: 0.25 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 815 5.04 %
Rwork0.183 --
obs0.185 16177 89.7 %
all-18077 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.31 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.1682 Å2-0 Å20 Å2
2---0.6 Å2-0 Å2
3---11.7682 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 2 86 3343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043312
X-RAY DIFFRACTIONf_angle_d0.8024470
X-RAY DIFFRACTIONf_dihedral_angle_d16.0471207
X-RAY DIFFRACTIONf_chiral_restr0.064486
X-RAY DIFFRACTIONf_plane_restr0.003572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4028-2.55340.28941000.20052044X-RAY DIFFRACTION73
2.5534-2.75050.23831300.18062343X-RAY DIFFRACTION84
2.7505-3.02710.25811470.1822541X-RAY DIFFRACTION90
3.0271-3.46490.23431450.18192692X-RAY DIFFRACTION95
3.4649-4.36440.20411500.16372780X-RAY DIFFRACTION97
4.3644-38.0270.22851430.19272963X-RAY DIFFRACTION97

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