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- PDB-1d0h: THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH N-ACETYL-GALACTOSAMINE -

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Basic information

Entry
Database: PDB / ID: 1d0h
TitleTHE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH N-ACETYL-GALACTOSAMINE
ComponentsPROTEIN (TETANUS TOXIN HC)
KeywordsTOXIN / 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
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / Tetanus toxin
Similarity search - Component
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASES FROM ISOMORPHOUS STRUCTURE, THE HC-LACTOSE COMPLEX / Resolution: 2.1 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. / Schmidt, J.J. / Sax, M.
History
DepositionSep 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 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

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Assembly

Deposited unit
A: PROTEIN (TETANUS TOXIN HC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3474
Polymers53,8081
Non-polymers5383
Water9,026501
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.076, 70.882, 122.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein PROTEIN (TETANUS TOXIN HC) / TENTOXYLYSIN


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
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
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: Sep 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMACrefinement
Adxvdata processing
CCP4(SCALA)data scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1764 5 %RANDOM
Rwork0.204 ---
obs0.205 34611 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 35 501 4099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.031
X-RAY DIFFRACTIONp_angle_deg
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
Rfactor obs: 0.204 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS

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