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- PDB-1dfq: THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH SIALIC ACID -

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Basic information

Entry
Database: PDB / ID: 1dfq
TitleTHE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH SIALIC ACID
ComponentsTETANUS TOXIN HC
KeywordsTOXIN / BETA TREFOIL / JELLY-ROLL / CARBOHYDRATE
Function / homology
Function and homology information


tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / symbiont-mediated suppression of host exocytosis / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis ...tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / symbiont-mediated suppression of host exocytosis / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / extracellular region / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-beta-neuraminic acid / Tetanus toxin
Similarity search - Component
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsEmsley, 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
DepositionNov 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETANUS TOXIN HC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1442
Polymers50,8351
Non-polymers3091
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.860, 70.240, 122.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TETANUS TOXIN HC


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
#2: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mg/mlprotein1drop
220 mMimidazole1drop
3100 mM1dropNaCl
4200 mMammonium sulfate1reservoir
540 %(w/v)PEG40001reservoir
61 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: USE OF MAXIMUM LIKELIHOOD REFINEMENT (REFMAC REFINEMENT PROGRAM)
RfactorNum. reflection% reflectionSelection details
Rfree0.313 739 -RANDOM
Rwork0.2 ---
obs0.2 14240 82 %-
all-14240 --
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 21 221 3805
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg0.05
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.042
X-RAY DIFFRACTIONp_angle_deg0.008

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