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Yorodumi- PDB-1d0h: THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH N-ACETYL-GALACTOSAMINE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d0h | |||||||||
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Title | THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH N-ACETYL-GALACTOSAMINE | |||||||||
Components | PROTEIN (TETANUS TOXIN HC) | |||||||||
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 / PHASES FROM ISOMORPHOUS STRUCTURE, THE HC-LACTOSE COMPLEX / Resolution: 2.1 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. / 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 | 1d0h.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d0h.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d0h_validation.pdf.gz | 463.6 KB | Display | wwPDB validaton report |
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Full document | 1d0h_full_validation.pdf.gz | 477.2 KB | Display | |
Data in XML | 1d0h_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 1d0h_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d0h ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d0h | HTTPS FTP |
-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: 53808.492 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN OF HEAVY CHAIN Mutation: ADDITION OF THE SEQUENCE MGHGHHHHHHHHHHSSGHIEGRHML AT THE N-TERMINAL RESIDUE 872 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 | ||||
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#2: Sugar | #3: Chemical | ChemComp-SO4 / | #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: 2.7 Å3/Da / Density % sol: 54.44 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
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: Sep 16, 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: 2.1→40 Å / Num. obs: 34754 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.1→2.19 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.665 / % possible all: 99.8 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Num. measured all: 238621 / Biso Wilson estimate: 26.9 Å2 |
Reflection shell | *PLUS Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: PHASES FROM ISOMORPHOUS STRUCTURE, THE HC-LACTOSE COMPLEX Resolution: 2.1→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: USE OF MAXIMUM LIKELIHOOD REFINEMENT AS IMPLEMENTED IN REFMAC
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.204 / Rfactor Rfree: 0.27 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |