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- PDB-1af9: TETANUS NEUROTOXIN C FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1af9
TitleTETANUS NEUROTOXIN C FRAGMENT
ComponentsTETANUS NEUROTOXIN
KeywordsCLOSTRIDIAL NEUROTOXIN / TETANUS / RECEPTOR BINDING
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
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.7 Å
AuthorsUmland, T.C. / Wingert, L. / Swaminathan, S. / Furey, W.F. / Schmidt, J.J. / Sax, M.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of Tetanus Neurotoxin C Fragment
Authors: Umland, T.C. / Wingert, L. / Swaminathan, S. / Schmidt, J.J. / Sax, M.
#2: Journal: Thesis, University of Pittsburgh / Year: 1994
Title: The Crystal Structures of Human and Rat Clara Cell Phospholipid Binding Proteins and the Preliminary Crystallographic Analysis of Botulinum E Neurotoxin and Tetanus Toxin C-Fragment
Authors: Umland, T.C.
History
DepositionMar 24, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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 NEUROTOXIN


Theoretical massNumber of molelcules
Total (without water)51,8261
Polymers51,8261
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.400, 79.700, 91.100
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 NEUROTOXIN


Mass: 51826.426 Da / Num. of mol.: 1 / Fragment: C FRAGMENT / Mutation: MET INSERTED AT N-TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetani (bacteria) / Description: PURCHASED FROM BOEHRINGER MANNHEIM / Production host: Escherichia coli (E. coli) / References: UniProt: P04958, tentoxilysin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.45 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.5
Details: CRYSTALLIZATION DROP CONTAINED 3 PARTS RESERVOIR SOLUTION AND 1 PART PROTEIN SOLUTION. RESERVOIR: 14%- 18% PEG 4000, 0.1M IMIDAZOLE, 0.05M MGCL2 AT PH 6.5. PROTEIN SOLUTION: 10MG/ML PROTEIN ...Details: CRYSTALLIZATION DROP CONTAINED 3 PARTS RESERVOIR SOLUTION AND 1 PART PROTEIN SOLUTION. RESERVOIR: 14%- 18% PEG 4000, 0.1M IMIDAZOLE, 0.05M MGCL2 AT PH 6.5. PROTEIN SOLUTION: 10MG/ML PROTEIN AND 0.01M TRIS-HCL AT PH 7.8.
PH range: 6.5-7.8
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, hanging drop
Details: Umland, T.C., (1998) Acta Crystallogr.,Sect.D, 54, 273.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.01 MTris-HCl1drop
214-18 %(w/v)PEG40001reservoir
30.1 Mimidazole1reservoir
40.05 M1reservoircan be replaced by NaCl or NaCH3CO2MgCl2

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1994 / Details: SUPPER DOUBLE MIRRORS
RadiationMonochromator: NI FILTER AND SUPPER DOUBLE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. obs: 14445 / % possible obs: 91.6 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.076 / Net I/σ(I): 54.8
Reflection shellResolution: 2.6→2.7 Å / % possible all: 59.7
Reflection
*PLUS
Num. measured all: 47673
Reflection shell
*PLUS
% possible obs: 71.2 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
WEISSMAN'S(MODIFIED LOCALLY)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.7→8 Å / Rfactor Rfree error: 0.0068 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1301 10.2 %RANDOM
Rwork0.161 ---
obs0.161 12771 95.4 %-
Displacement parametersBiso mean: 15.6 Å2
Refine analyzeLuzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 0 138 3702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.225 132 10.4 %
Rwork0.206 1273 -
obs--85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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