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Yorodumi- PDB-7z5s: Crystal Structure of botulinum neurotoxin A2 cell binding domain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z5s | ||||||
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Title | Crystal Structure of botulinum neurotoxin A2 cell binding domain in complex with GD1a | ||||||
Components | Botulinum neurotoxin | ||||||
Keywords | TOXIN / ganglioside / neurotoxin / botulinum / receptor / GD1a | ||||||
Function / homology | Function and homology information negative regulation of neurotransmitter secretion / 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: 2.1 Å | ||||||
Authors | Gregory, K.S. / Acharya, K.R. / Liu, S.M. / Mahadeva, T.B. | ||||||
Funding support | 1items
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Citation | Journal: Toxins / Year: 2022 Title: Structural Features of Clostridium botulinum Neurotoxin Subtype A2 Cell Binding Domain. Authors: Gregory, K.S. / Mahadeva, T.B. / Liu, S.M. / Acharya, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z5s.cif.gz | 193.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z5s.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z5s_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7z5s_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7z5s_validation.xml.gz | 34 KB | Display | |
Data in CIF | 7z5s_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/7z5s ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z5s | HTTPS FTP |
-Related structure data
Related structure data | 7z5tC 5moyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50416.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: A, bont / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4GGE0 #2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | 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: 3.63 Å3/Da / Density % sol: 66.1 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium citrate tribasic tetrahydrate 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→105.07 Å / Num. obs: 83782 / % possible obs: 100 % / Redundancy: 27.3 % / CC1/2: 0.99 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 21.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4633 / CC1/2: 0.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MOY Resolution: 2.1→105.068 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.159 / Average fsc free: 0.8683 / Average fsc work: 0.8793 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.145 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.052 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→105.068 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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