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- PDB-7bxx: Tetanus neurotoxin translocation domain -C467S -

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Basic information

Entry
Database: PDB / ID: 7bxx
TitleTetanus neurotoxin translocation domain -C467S
ComponentsTetanus toxinTetanospasmin
KeywordsTOXIN / Tetanus neurotoxin translocation domain
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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsZhang, C.M. / Imoto, Y. / Fukuda, Y. / Yamashita, E. / Inoue, T.
CitationJournal: J Struct Biol X / Year: 2021
Title: Structural flexibility of the tetanus neurotoxin revealed by crystallographic and solution scattering analyses.
Authors: Zhang, C.M. / Imoto, Y. / Hikima, T. / Inoue, T.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetanus toxin
B: Tetanus toxin


Theoretical massNumber of molelcules
Total (without water)93,2262
Polymers93,2262
Non-polymers00
Water1,44180
1
A: Tetanus toxin


Theoretical massNumber of molelcules
Total (without water)46,6131
Polymers46,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tetanus toxin


Theoretical massNumber of molelcules
Total (without water)46,6131
Polymers46,6131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.596, 107.121, 211.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tetanus toxin / Tetanospasmin / Tentoxylysin


Mass: 46613.074 Da / Num. of mol.: 2 / Mutation: C467S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetani (strain Massachusetts / E88) (bacteria)
Strain: Massachusetts / E88 / Gene: tetX, CTC_p60 / Production host: Escherichia coli (E. coli) / References: UniProt: P04958, tentoxilysin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.225M MES/Bis-Tris pH 6.6, 6.6% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.34→47.78 Å / Num. obs: 38647 / % possible obs: 99.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 57.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.031 / Net I/σ(I): 11.5
Reflection shellResolution: 2.34→2.43 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3555 / CC1/2: 0.888 / Rpim(I) all: 0.395 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N0B(550-864)

5n0b


Resolution: 2.34→38.92 Å / SU ML: 0.3876 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.5583
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 1998 5.19 %
Rwork0.2087 36533 -
obs0.211 38531 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.88 Å2
Refinement stepCycle: LAST / Resolution: 2.34→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4800 0 0 80 4880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00934891
X-RAY DIFFRACTIONf_angle_d1.09896604
X-RAY DIFFRACTIONf_chiral_restr0.0588761
X-RAY DIFFRACTIONf_plane_restr0.0073826
X-RAY DIFFRACTIONf_dihedral_angle_d18.0563639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.40.4251300.40742365X-RAY DIFFRACTION92.99
2.4-2.470.40531430.35752625X-RAY DIFFRACTION99.6
2.47-2.540.36931390.32832530X-RAY DIFFRACTION99.85
2.54-2.620.33551430.30292617X-RAY DIFFRACTION99.67
2.62-2.720.34931410.27982565X-RAY DIFFRACTION99.6
2.72-2.830.35721430.28792623X-RAY DIFFRACTION99.68
2.83-2.950.30041400.25722565X-RAY DIFFRACTION99.82
2.95-3.110.31261430.25872601X-RAY DIFFRACTION99.82
3.11-3.30.31421450.25452650X-RAY DIFFRACTION99.96
3.3-3.560.27711430.24452614X-RAY DIFFRACTION99.89
3.56-3.920.23281450.19052652X-RAY DIFFRACTION99.82
3.92-4.480.21091440.16772634X-RAY DIFFRACTION99.43
4.48-5.640.17831480.15232701X-RAY DIFFRACTION99.41
5.65-38.920.22231510.16662791X-RAY DIFFRACTION98.07
Refinement TLS params.Method: refined / Origin x: -24.9820230363 Å / Origin y: -1.47644875648 Å / Origin z: 11.7249689839 Å
111213212223313233
T0.437044219344 Å2-0.0135532507644 Å2-0.0251741736088 Å2-0.419810270049 Å2-0.0510110402328 Å2--0.470396054362 Å2
L0.190366656163 °20.090693867074 °20.20459071045 °2-0.314332756384 °2-0.0720080518011 °2--1.28142805485 °2
S-0.10767161163 Å °-0.00792571566102 Å °0.0445681212915 Å °0.0299131248651 Å °0.0233516570141 Å °-0.0302613740582 Å °-0.341141035983 Å °-0.0557738479996 Å °0.0654490079418 Å °
Refinement TLS groupSelection details: all

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