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- PDB-3k3q: Crystal Structure of a Llama Antibody complexed with the C. Botul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k3q | ||||||
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Title | Crystal Structure of a Llama Antibody complexed with the C. Botulinum Neurotoxin Serotype A Catalytic Domain | ||||||
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![]() | IMMUNE SYSTEM / llama / VHH / antibody / botulinum / neurotoxin / BoNT / Cell junction / Cell membrane / Cytoplasm / Disulfide bond / Hydrolase / Membrane / Metal-binding / Metalloprotease / Pharmaceutical / Protease / Secreted / Synapse / Toxin / Transmembrane / Zinc | ||||||
Function / homology | ![]() host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Thompson, A.A. / Dong, J. / Marks, J.D. / Stevens, R.C. | ||||||
![]() | ![]() Title: A Single-Domain Llama Antibody Potently Inhibits the Enzymatic Activity of Botulinum Neurotoxin by Binding to the Non-Catalytic alpha-Exosite Binding Region. Authors: Dong, J. / Thompson, A.A. / Fan, Y. / Lou, J. / Conrad, F. / Ho, M. / Pires-Alves, M. / Wilson, B.A. / Stevens, R.C. / Marks, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119 KB | Display | ![]() |
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PDB format | ![]() | 95.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.6 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Details | Authors state it is possible that a hexamer exists in solution, but this would be in equilibrium with the trimer. |
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Components
#1: Protein | Mass: 16147.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 28359.986 Da / Num. of mol.: 1 Fragment: N-terminal fragment of BoNT catalytic domain (residues 3-250) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: botA, CBO0806, CLC_0862, neurotoxin catalytic domain / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin |
#3: Protein | Mass: 20621.465 Da / Num. of mol.: 1 Fragment: C-terminal fragment of BoNT catalytic domain (residues 251-425) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: botA, CBO0806, CLC_0862, neurotoxin catalytic domain / Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin |
#4: Chemical | ChemComp-ZN / |
#5: Water | ChemComp-HOH / |
Sequence details | THERE IS A VAL -> ALA NATURAL VARIANT AT RESIDUE 27. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2.8 % / Av σ(I) over netI: 7.33 / Number: 64075 / Rmerge(I) obs: 0.117 / Χ2: 1 / D res high: 2.6 Å / D res low: 40 Å / Num. obs: 22641 / % possible obs: 96.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.6→40 Å / Num. obs: 22641 / % possible obs: 96.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.117 / Χ2: 0.995 / Net I/σ(I): 9.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.16 / Num. unique all: 977 / Χ2: 1.003 / % possible all: 83.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 20.541 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 91.81 Å2 / Biso mean: 41.719 Å2 / Biso min: 3.39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→40 Å
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Refine LS restraints |
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Xplor file |
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