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

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Basic information

Entry
Database: PDB / ID: 7kyh
TitleBotulism Neurooxin Light Chain A app form
ComponentsBont/A1
KeywordsTOXIN / BoNT
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
Chem-XBM / Bontoxilysin-A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)193,32312
Polymers191,1084
Non-polymers2,2158
Water00
1
A: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3313
Polymers47,7771
Non-polymers5542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3313
Polymers47,7771
Non-polymers5542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3313
Polymers47,7771
Non-polymers5542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3313
Polymers47,7771
Non-polymers5542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.315, 84.050, 99.723
Angle α, β, γ (deg.)103.780, 91.840, 108.670
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bont/A1


Mass: 47777.039 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-XBM / N-[(3,5-dichlorophenyl)sulfonyl]-L-phenylalanyl-N-hydroxy-L-valinamide


Mass: 488.385 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23Cl2N3O5S / Feature type: SUBJECT OF INVESTIGATION
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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 50mM sodium cacodylate pH 7.0, 200 mM 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, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.91→48.14 Å / Num. obs: 35479 / % possible obs: 95.14 % / Redundancy: 1.9 % / CC1/2: 0.991 / Net I/σ(I): 2.6
Reflection shellResolution: 2.91→9.09 Å / Num. unique obs: 112823 / CC1/2: 0.998

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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: 2.91→48.09 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.309 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2297 6.5 %RANDOM
Rwork0.1377 ---
obs0.1399 33183 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 241.45 Å2 / Biso mean: 62.611 Å2 / Biso min: 2.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20.03 Å20.26 Å2
2--0.23 Å20.11 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.91→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12508 0 128 0 12636
Biso mean--18.88 --
Num. residues----1540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01312924
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711824
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.66317480
X-RAY DIFFRACTIONr_angle_other_deg1.0861.58827508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6451524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02923.801684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.603152228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7811548
X-RAY DIFFRACTIONr_chiral_restr0.070.21684
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022752
LS refinement shellResolution: 2.91→2.985 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.535 212 -
Rwork0.615 1930 -
all-2142 -
obs--77.36 %

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