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Yorodumi- PDB-5l21: Crystal structure of BoNT/A receptor binding domain in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l21 | ||||||
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Title | Crystal structure of BoNT/A receptor binding domain in complex with VHH C2 | ||||||
Components |
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Keywords | TOXIN / Neutralizing antibody / VHH / Botulinum neurotoxin / BoNT-A-VHH complex | ||||||
Function / homology | Function and homology information 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 | Clostridium botulinum (bacteria) Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Yao, G. / Jin, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2017 Title: A camelid single-domain antibody neutralizes botulinum neurotoxin A by blocking host receptor binding. Authors: Yao, G. / Lam, K.H. / Weisemann, J. / Peng, L. / Krez, N. / Perry, K. / Shoemaker, C.B. / Dong, M. / Rummel, A. / Jin, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l21.cif.gz | 249.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l21.ent.gz | 197.5 KB | Display | PDB format |
PDBx/mmJSON format | 5l21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l21_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 5l21_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 5l21_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 5l21_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/5l21 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/5l21 | HTTPS FTP |
-Related structure data
Related structure data | 3fuoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49877.488 Da / Num. of mol.: 1 / Mutation: T1158A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A) (bacteria) Strain: Hall / ATCC 3502 / NCTC 13319 / Type A / Gene: botA, CBO0806, CLC_0862 / Production host: Escherichia coli (E. coli) References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin |
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#2: Antibody | Mass: 13326.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 18% polyethylene glycol 6,000; 100 mM Sodium Acetate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→35.99 Å / Num. obs: 74608 / % possible obs: 99.5 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.843 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FUO Resolution: 1.68→35.99 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→35.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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