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- PDB-7by5: Tetanus neurotoxin mutant-(H233A/E234Q/H237A/Y375F) -

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Basic information

Entry
Database: PDB / ID: 7by5
TitleTetanus neurotoxin mutant-(H233A/E234Q/H237A/Y375F)
ComponentsTetanus toxinTetanospasmin
KeywordsTOXIN / Neurotoxin
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetanus toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,49614
Polymers151,6561
Non-polymers83913
Water13,908772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.542, 145.542, 129.038
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2195-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Tetanus toxin / Tetanospasmin / Tentoxylysin


Mass: 151656.484 Da / Num. of mol.: 1 / Mutation: H233A,E234Q,H237A,Y375F
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 BL21(DE3) (bacteria) / References: UniProt: P04958, tentoxilysin

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Non-polymers , 5 types, 785 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M MOPS pH 7.0, 9% PEG 8000

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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: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.27→48.28 Å / Num. obs: 72360 / % possible obs: 99.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.053 / Rrim(I) all: 0.137 / Net I/σ(I): 10.7
Reflection shellResolution: 2.27→2.32 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4203 / CC1/2: 0.634 / Rpim(I) all: 0.446 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z7H, 1AF9, 5N0B

1z7h

1af9

5n0b


Resolution: 2.27→48.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.218
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3663 5.063 %Random
Rwork0.186 68690 --
all0.188 ---
obs0.186 72353 99.1 %-
Solvent computationVDW probe radii: 64.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 59.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.27→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10393 0 51 772 11216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01210740
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.63614547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29451303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19524.45555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.358151933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2911537
X-RAY DIFFRACTIONr_chiral_restr0.0780.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028135
X-RAY DIFFRACTIONr_nbd_refined0.1910.24897
X-RAY DIFFRACTIONr_nbtor_refined0.3070.27378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2696
X-RAY DIFFRACTIONr_metal_ion_refined0.1830.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.26
X-RAY DIFFRACTIONr_mcbond_it2.4155.7965179
X-RAY DIFFRACTIONr_mcangle_it3.718.6846481
X-RAY DIFFRACTIONr_scbond_it2.9615.9955560
X-RAY DIFFRACTIONr_scangle_it4.378.8798061
X-RAY DIFFRACTIONr_lrange_it6.78678.63216595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.271-2.330.3432340.2854868X-RAY DIFFRACTION95.56
2.33-2.3930.3112830.2574845X-RAY DIFFRACTION98.6913
2.393-2.4630.2972520.2284788X-RAY DIFFRACTION99.3103
2.463-2.5380.2492490.2164600X-RAY DIFFRACTION98.7576
2.538-2.6210.2592200.1974529X-RAY DIFFRACTION99.2684
2.621-2.7130.2762480.1924311X-RAY DIFFRACTION99.1518
2.713-2.8150.2672360.1924219X-RAY DIFFRACTION99.1763
2.815-2.9290.282290.1874028X-RAY DIFFRACTION99.4162
2.929-3.0590.2441790.1793938X-RAY DIFFRACTION99.5406
3.059-3.2080.2352110.1613712X-RAY DIFFRACTION99.3919
3.208-3.3810.232100.1673550X-RAY DIFFRACTION99.3395
3.381-3.5850.2171640.163371X-RAY DIFFRACTION99.4094
3.585-3.830.2331720.1593201X-RAY DIFFRACTION99.6161
3.83-4.1350.1941540.1572970X-RAY DIFFRACTION99.7446
4.135-4.5270.1851410.1622743X-RAY DIFFRACTION99.6545
4.527-5.0550.2031320.1562498X-RAY DIFFRACTION99.6967
5.055-5.8270.2281100.2152229X-RAY DIFFRACTION99.8719
5.827-7.110.343860.2481906X-RAY DIFFRACTION99.7996
7.11-9.9480.2940.1851487X-RAY DIFFRACTION99.8737

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