+Open data
-Basic information
Entry | Database: PDB / ID: 7kyh | ||||||
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Title | Botulism Neurooxin Light Chain A app form | ||||||
Components | Bont/A1 | ||||||
Keywords | TOXIN / BoNT | ||||||
Function / homology | Function and homology information protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Ortega, M.E. / Salzameda, N.T. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kyh.cif.gz | 317.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kyh.ent.gz | 259.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kyh_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7kyh_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7kyh_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 7kyh_validation.cif.gz | 57.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/7kyh ftp://data.pdbj.org/pub/pdb/validation_reports/ky/7kyh | HTTPS FTP |
-Related structure data
Related structure data | 7ky2C 7kyfC 4hevS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | 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 / #3: Chemical | ChemComp-XBM / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 50mM sodium cacodylate pH 7.0, 200 mM ammonium sulfate, 30% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.91→9.09 Å / Num. unique obs: 112823 / CC1/2: 0.998 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 241.45 Å2 / Biso mean: 62.611 Å2 / Biso min: 2.61 Å2
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Refinement step | Cycle: final / Resolution: 2.91→48.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.91→2.985 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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