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- PDB-7ky2: Botulism Neurooxin Light Chain A app form -

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Basic information

Entry
Database: PDB / ID: 7ky2
TitleBotulism Neurooxin Light Chain A app form
ComponentsBont/A1
KeywordsTOXIN / BoNT / botulinum neurotoxin apo form
Function / homology
Function and homology information


protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsOrtega, M.E. / Salazameda, 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

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Assembly

Deposited unit
A: Bont/A1
B: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1314
Polymers98,0012
Non-polymers1312
Water34219
1
A: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0662
Polymers49,0001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0662
Polymers49,0001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.029, 56.985, 192.136
Angle α, β, γ (deg.)90.000, 90.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bont/A1


Mass: 49000.250 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium cacodylate pH 7.0, 200 mM ammonium sulfate, and 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: 0.9763 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.66→49.01 Å / Num. obs: 21424 / % possible obs: 99.32 % / Redundancy: 1 % / CC1/2: 0.967 / Net I/σ(I): 4.4

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Processing

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

4hev


Resolution: 2.78→49.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.694 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1698 693 3.2 %RANDOM
Rwork0.128 ---
obs0.1294 20732 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.48 Å2 / Biso mean: 47.493 Å2 / Biso min: 19.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.03 Å2
2--0.02 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.78→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 2 19 6419
Biso mean--180.23 30 -
Num. residues----786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136542
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176016
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.6488832
X-RAY DIFFRACTIONr_angle_other_deg1.2931.57913996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9095774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58423.672354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.339151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2621526
X-RAY DIFFRACTIONr_chiral_restr0.0810.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027214
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021392
LS refinement shellResolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.753 45 -
Rwork0.665 1512 -
all-1557 -
obs--99.87 %

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