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- PDB-7kyf: Botulism Neurooxin Light Chain A app form -

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Basic information

Entry
Database: PDB / ID: 7kyf
TitleBotulism Neurooxin Light Chain A app form
ComponentsBont/A1
KeywordsTOXIN / BoNT / botulinum neurotoxin nva-ila dipetpide bound
Function / homology
Function and homology information


protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
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 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
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsOrtega, M.E. / Salzameda, N.T.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Discovery of Dipeptides as Potent Botulinum Neurotoxin A Light-Chain Inhibitors.
Authors: Amezcua, M. / Cruz, R.S. / Ku, A. / Moran, W. / Ortega, M.E. / Salzameda, N.T.
History
DepositionDec 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
C: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2973
Polymers47,7771
Non-polymers5202
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.527, 196.401, 38.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bont/A1


Mass: 47777.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C6K838
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-XC1 / N-[(3,5-dichlorophenyl)sulfonyl]-L-isoleucyl-N-hydroxy-L-norvalinamide


Mass: 454.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25Cl2N3O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50mM sodium cacodylate pH 7.0, 200mM ammonium sulfate, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→43.25 Å / Num. obs: 19587 / % possible obs: 93.2 % / Redundancy: 1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hev

4hev


Resolution: 2.33→43.25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.217 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1959 10 %RANDOM
Rwork0.1604 ---
obs0.1623 17628 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 356.19 Å2 / Biso mean: 55.137 Å2 / Biso min: 8.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.05 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 2.33→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 29 19 3275
Biso mean--30.89 30 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0133327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173056
X-RAY DIFFRACTIONr_angle_refined_deg2.1941.6614497
X-RAY DIFFRACTIONr_angle_other_deg1.1741.597108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5065393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0723.729177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.31115575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4471513
X-RAY DIFFRACTIONr_chiral_restr0.1420.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023666
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02705
LS refinement shellResolution: 2.33→2.391 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 141 -
Rwork0.426 1275 -
all-1416 -
obs--99.65 %

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