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Yorodumi- PDB-3zuq: Crystal structure of an engineered botulinum neurotoxin type B - ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zuq | ||||||
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Title | Crystal structure of an engineered botulinum neurotoxin type B - derivative, LC-B-GS-Hn-B | ||||||
Components | BOTULINUM NEUROTOXIN TYPE B | ||||||
Keywords | HYDROLASE / PROTEIN ENGINEERING | ||||||
Function / homology | Function and homology information Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | CLOSTRIDIUM BOTULINUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Masuyer, G. / Stancombe, P. / Chaddock, J.A. / Acharya, K.R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Structures of Engineered Clostridium Botulinum Neurotoxin Derivatives Authors: Masuyer, G. / Stancombe, P. / Chaddock, J.A. / 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 | 3zuq.cif.gz | 343.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zuq.ent.gz | 280.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zuq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/3zuq ftp://data.pdbj.org/pub/pdb/validation_reports/zu/3zuq | HTTPS FTP |
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-Related structure data
Related structure data | 3zurC 3zusC 2xhlS 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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Unit cell |
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-Components
#1: Protein | Mass: 102777.094 Da / Num. of mol.: 1 Fragment: CATALYTIC DOMAIN, RESIDUES 1-437, TRANSLOCATION DOMAIN, RESIDUES 446-858 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10844, bontoxilysin |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Sequence details | REPEATS GGGGS LINKERS ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.1M TRIS ACETATE PH8.0, 0.2M MGCL, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.28 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→58.4 Å / Num. obs: 28039 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XHL Resolution: 2.7→77.03 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.867 / SU B: 28.855 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 440-476 MISSING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.442 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→77.03 Å
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