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Yorodumi- PDB-2xhl: Structure of a functional derivative of Clostridium botulinum neu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xhl | |||||||||
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Title | Structure of a functional derivative of Clostridium botulinum neurotoxin type B | |||||||||
Components |
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Keywords | HYDROLASE / METALLOPROTEASE / MEMBRANE DOMAIN / ENDOPEPTIDASE / ZINC PROTEASE / BOTULISM / TOXIN | |||||||||
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: 2.8 Å | |||||||||
Authors | Masuyer, G. / Beard, M. / Cadd, V.A. / Chaddock, J.A. / Acharya, K.R. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Structure and Activity of a Functional Derivative of Clostridium Botulinum Neurotoxin B. Authors: Masuyer, G. / Beard, M. / Cadd, V.A. / 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 | 2xhl.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xhl.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/2xhl ftp://data.pdbj.org/pub/pdb/validation_reports/xh/2xhl | HTTPS FTP |
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-Related structure data
Related structure data | 1epwS 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: 52291.562 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-437 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: MODIFIED PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P10844, bontoxilysin |
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#2: Protein | Mass: 49759.141 Da / Num. of mol.: 1 / Fragment: RESIDUES 446-858 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: MODIFIED PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P10844 |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
Sequence details | OWING TO THE PRESENCE OF AN INTERNAL EXPRESSION TAG FOR CLEAVAGE BETWEEN THE TWO CHAINS THE ...OWING TO THE PRESENCE OF AN INTERNAL EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 57 % / Description: NONE |
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Crystal grow | pH: 7.2 Details: 15% PEG3350, 0.1M BIS-TRIS-PROPANE PH 6.5, 0.2M SODIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.64 Å / Num. obs: 28644 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EPW Resolution: 2.8→113.49 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.853 / SU B: 33.922 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 208-218,626-630 ARE DISORDERED.
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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: 36.557 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→113.49 Å
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Refine LS restraints |
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