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- PDB-1yvg: Structural analysis of the catalytic domain of tetanus neurotoxin -

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Basic information

Entry
Database: PDB / ID: 1yvg
TitleStructural analysis of the catalytic domain of tetanus neurotoxin
ComponentsTetanus toxin, light chainTetanospasmin
KeywordsHYDROLASE / Clostridium neurotoxins / tetanus neurotoxin / zinc metalloprotease / Dual-wavelength Anomalous dispersion (DAD)
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
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, Molecular replacement / Resolution: 2.6 Å
AuthorsRao, K.N. / Kumaran, D. / Binz, T. / Swaminathan, S.
CitationJournal: Toxicon / Year: 2005
Title: Structural analysis of the catalytic domain of tetanus neurotoxin.
Authors: Rao, K.N. / Kumaran, D. / Binz, T. / Swaminathan, S.
History
DepositionFeb 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetanus toxin, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7652
Polymers53,7001
Non-polymers651
Water2,036113
1
A: Tetanus toxin, light chain
hetero molecules

A: Tetanus toxin, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5304
Polymers107,3992
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.610, 177.280, 54.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Cell settingorthorhombic
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-572-

HOH

DetailsDimer, The second part of the biological assembly is generated by the crystallographic two fold axis

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Components

#1: Protein Tetanus toxin, light chain / Tetanospasmin / E.C.3.4.24.68 / Tentoxylysin / light chain


Mass: 53699.531 Da / Num. of mol.: 1 / Fragment: chain L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetani (bacteria) / Gene: tetX / Production host: Escherichia coli (E. coli) / References: UniProt: P04958, tentoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 4000, magnesium chloride, hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11.2810, 1.2824
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDateDetails
BRANDEIS - B41CCDMay 1, 2004Mirrors
ADSC QUANTUM 3152CCDSep 17, 2004Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.2811
21.28241
31.11
ReflectionResolution: 2.4→50 Å / Num. all: 20639 / Num. obs: 20639 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.12 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 7 / Num. unique all: 2001 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
SOLVE& SHARPphasing
CNS1refinement
SHARPphasing
RefinementMethod to determine structure: MAD, Molecular replacement
Starting model: 1F82

1f82


Resolution: 2.6→50 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2763 1033 6.8 %Random
Rwork0.2182 ---
all-15170 --
obs-15170 92.7 %-
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-13.339 Å20 Å20 Å2
2--20.489 Å20 Å2
3----33.828 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 1 113 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008306
X-RAY DIFFRACTIONc_angle_deg1.36447
X-RAY DIFFRACTIONc_mcbond_it1.1141.5
X-RAY DIFFRACTIONc_mcangle_it1.9182
X-RAY DIFFRACTIONc_scbond_it1.4882
X-RAY DIFFRACTIONc_scangle_it2.3382.5
LS refinement shellResolution: 2.6→2.64 Å
RfactorNum. reflection
Rfree0.4239 49
Rwork0.3592 -
obs-558

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