+Open data
-Basic information
Entry | Database: PDB / ID: 1dll | |||||||||
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Title | The HC fragement of tetanus toxin complexed with lactose | |||||||||
Components | TETANUS TOXINTetanospasmin | |||||||||
Keywords | TOXIN / Beta trefoil / Jelly roll | |||||||||
Function / homology | Function and homology information tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding ...tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding / extracellular region / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Clostridium tetani (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Emsley, P. / Fotinou, C. / Black, I. / Fairweather, N.F. / Charles, I.G. / Watts, C. / Hewitt, E. / Isaacs, N.W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: The structures of the H(C) fragment of tetanus toxin with carbohydrate subunit complexes provide insight into ganglioside binding. Authors: Emsley, P. / Fotinou, C. / Black, I. / Fairweather, N.F. / Charles, I.G. / Watts, C. / Hewitt, E. / Isaacs, N.W. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of the Receptor Binding Fragment HC of Tetanus Neurotoxin Authors: Umland, T.C. / Wingert, L.M. / Swaminathan, S. / Fury, W.F. / Schmitt, J.J. / Sax, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dll.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dll.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/1dll ftp://data.pdbj.org/pub/pdb/validation_reports/dl/1dll | HTTPS FTP |
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-Related 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: 50476.918 Da / Num. of mol.: 1 / Fragment: RECEPTOR BINDING FRAGMENT HC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetani (bacteria) / Plasmid: PET 16B / Production host: Escherichia coli (E. coli) / References: UniProt: P04958, tentoxilysin | ||
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose | ||
#3: Chemical | ChemComp-GOL / #4: 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: 2.88 Å3/Da / Density % sol: 57.26 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: imidazole, sodium chloride, ammonium sulphate, PEG4000, 2-methyl-2,4-pentane-diol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 226864 / Num. obs: 54336 / % possible obs: 99.4 % / Observed criterion σ(F): -467.3 / Observed criterion σ(I): -702.5 / Redundancy: 4.2 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.634 / Num. unique all: 3951 / % possible all: 58.2 |
Reflection | *PLUS Num. measured all: 226864 |
Reflection shell | *PLUS Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Resolution: 1.8→30 Å / σ(F): -456.3 / σ(I): -702.5 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Rfactor obs: 0.201 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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