+Open data
-Basic information
Entry | Database: PDB / ID: 1dfq | ||||||
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Title | THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH SIALIC ACID | ||||||
Components | TETANUS TOXIN HC | ||||||
Keywords | TOXIN / BETA TREFOIL / JELLY-ROLL / CARBOHYDRATE | ||||||
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: 2.6 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. / Furey, W.F. / Schmidt, 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 | 1dfq.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dfq.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 1dfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/1dfq ftp://data.pdbj.org/pub/pdb/validation_reports/df/1dfq | 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: 50835.223 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN OF HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium tetani (bacteria) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / References: UniProt: P04958, tentoxilysin |
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#2: Sugar | ChemComp-SLB / |
#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: 2.83 Å3/Da / Density % sol: 56.52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: IMIDAZOLE, SODIUM CHLORIDE, AMMONIUM SULFATE, 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: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 15003 / Num. obs: 15003 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.641 / % possible all: 82 |
Reflection | *PLUS Redundancy: 1.9 % / Num. measured all: 35496 |
Reflection shell | *PLUS Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: USE OF MAXIMUM LIKELIHOOD REFINEMENT (REFMAC REFINEMENT PROGRAM)
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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