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Yorodumi- PDB-7qpu: Botulinum neurotoxin A5 cell binding domain in complex with GM1b ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qpu | ||||||
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Title | Botulinum neurotoxin A5 cell binding domain in complex with GM1b oligosaccharide | ||||||
Components | Botulinum neurotoxin sub-type A5 | ||||||
Keywords | TOXIN / Cell binding domain / receptor / oligosaccharide / neurotoxin | ||||||
Function / homology | Function and homology information negative regulation of neurotransmitter secretion / bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Gregory, K.S. / Acharya, K.R. / Liu, S.M. | ||||||
Funding support | 1items
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Citation | Journal: Toxins / Year: 2022 Title: Crystal Structures of Botulinum Neurotoxin Subtypes A4 and A5 Cell Binding Domains in Complex with Receptor Ganglioside. Authors: Gregory, K.S. / Mojanaga, O.O. / 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 | 7qpu.cif.gz | 208.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qpu.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 7qpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/7qpu ftp://data.pdbj.org/pub/pdb/validation_reports/qp/7qpu | HTTPS FTP |
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-Related structure data
Related structure data | 7qptC 6twpS 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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Unit cell |
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-Components
#1: Protein | Mass: 50719.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: cntA, cntA/A5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1IPK2, bontoxilysin #2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-SO4 / | #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: 2.17 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 150 mM Li2SO4, 50 mM MgCl2 6H2O , 0.1 M HEPES pH 7.8, 4.7% w/v PEG 8K, 4.7% PEG 10K and 4.7% PEG 8K |
-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 X 16M / Detector: PIXEL / Date: Mar 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→129.4 Å / Num. obs: 33451 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.982 / Rpim(I) all: 0.126 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 22543 / CC1/2: 0.575 / Rpim(I) all: 0.746 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TWP Resolution: 2.4→76.07 Å / SU ML: 0.3514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2652 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→76.07 Å
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Refine LS restraints |
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LS refinement shell |
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