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- PDB-8ow8: Crystal Structure of the Catalytic Domain of a Botulinum Neurotox... -

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Basic information

Entry
Database: PDB / ID: 8ow8
TitleCrystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium
ComponentsBotulinum-like toxin eBoNT/J light chain
KeywordsTOXIN / Botulinum neurotoxin / homologue / enterococcus faecium
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion / bontoxilysin / host cell cytosol / protein transmembrane transporter activity / host cell cytoplasmic vesicle membrane / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding ...negative regulation of neurotransmitter secretion / bontoxilysin / host cell cytosol / protein transmembrane transporter activity / host cell cytoplasmic vesicle membrane / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
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, 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
TRIETHYLENE GLYCOL / PHOSPHATE ION / Botulinum-like toxin eBoNT/J
Similarity search - Component
Biological speciesEnterococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium : Potential Insights into Substrate Recognition.
Authors: Gregory, K.S. / Hall, P.R. / Onuh, J.P. / Mojanaga, O.O. / Liu, S.M. / Acharya, K.R.
History
DepositionApr 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum-like toxin eBoNT/J light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2116
Polymers50,7441
Non-polymers4685
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-49 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.894, 143.894, 51.695
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Botulinum-like toxin eBoNT/J light chain / LC


Mass: 50743.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus (bacteria) / Gene: A5816_002916 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A242DI27, bontoxilysin

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Non-polymers , 5 types, 161 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M SPG (succinic acid, sodium phosphate monobasic monohydrate, and glycine) buffer pH 7.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→143.89 Å / Num. obs: 37319 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.036 / Rrim(I) all: 0.134 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 26.6 % / Rmerge(I) obs: 3.807 / Num. unique obs: 2683 / CC1/2: 0.626 / Rpim(I) all: 1.06 / Rrim(I) all: 3.952

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
REFMAC5.8.0419refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→64.434 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.177 / SU B: 10.517 / SU ML: 0.139 / Average fsc free: 0.951 / Average fsc work: 0.9613 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 1882 5.051 %RANDOM
Rwork0.1883 35375 --
all0.19 ---
obs-37257 99.944 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.903 Å2
Baniso -1Baniso -2Baniso -3
1-1.266 Å2-0 Å20 Å2
2--1.266 Å20 Å2
3----2.532 Å2
Refinement stepCycle: LAST / Resolution: 2→64.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 25 156 3399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163151
X-RAY DIFFRACTIONr_angle_refined_deg1.911.6594489
X-RAY DIFFRACTIONr_angle_other_deg0.6061.5787285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4495401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.224513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22610593
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.23210156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
X-RAY DIFFRACTIONr_nbd_refined0.2260.2654
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.23022
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21674
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21809
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2164
X-RAY DIFFRACTIONr_metal_ion_refined0.2080.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0930.217
X-RAY DIFFRACTIONr_nbd_other0.1970.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.190.24
X-RAY DIFFRACTIONr_mcbond_it3.9123.8081604
X-RAY DIFFRACTIONr_mcbond_other3.9123.8081604
X-RAY DIFFRACTIONr_mcangle_it5.276.8222002
X-RAY DIFFRACTIONr_mcangle_other5.2696.8252003
X-RAY DIFFRACTIONr_scbond_it4.9044.1761715
X-RAY DIFFRACTIONr_scbond_other4.9034.1781716
X-RAY DIFFRACTIONr_scangle_it6.6717.4832486
X-RAY DIFFRACTIONr_scangle_other6.677.4842487
X-RAY DIFFRACTIONr_lrange_it8.20736.4533720
X-RAY DIFFRACTIONr_lrange_other8.20736.4583721
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3491410.33825340.33926810.90.89599.77620.339
2.052-2.1080.3071140.31425200.31326350.9060.91199.96210.311
2.108-2.1690.2751420.28224210.28225630.9440.9351000.277
2.169-2.2360.2541190.2424040.24125230.9520.9561000.23
2.236-2.3090.271290.22822760.23124060.9550.96399.95840.216
2.309-2.390.3041130.21922380.22323520.9490.96899.95750.205
2.39-2.480.2791050.2221750.22322810.9540.97299.95620.201
2.48-2.5810.3081120.21920760.22321890.9430.97299.95430.199
2.581-2.6960.326970.21619870.22120840.9420.9731000.197
2.696-2.8270.249830.20519500.20720340.9630.97799.95080.186
2.827-2.980.266950.21318120.21619070.9470.9731000.197
2.98-3.160.281040.21317310.21718350.9520.9721000.2
3.16-3.3770.255920.22316170.22517090.9660.9741000.214
3.377-3.6470.231920.20115320.20316240.9690.9821000.196
3.647-3.9940.19850.17814110.17914960.9770.9861000.174
3.994-4.4630.177720.13412770.13613490.9830.991000.132
4.463-5.150.157570.11311600.11512170.990.9931000.113
5.15-6.2970.168390.1529970.15310360.9840.9881000.152
6.297-8.8630.186580.1497830.1518410.9810.9881000.15
8.863-64.4340.188330.2114740.215090.980.96299.60710.215
Refinement TLS params.Method: refined / Origin x: 43.8046 Å / Origin y: -16.8654 Å / Origin z: 18.0325 Å
111213212223313233
T0.118 Å2-0.0687 Å20.0178 Å2-0.1724 Å20.0013 Å2--0.0176 Å2
L1.4734 °2-0.3734 °2-0.357 °2-1.3435 °20.1597 °2--1.5572 °2
S-0.0343 Å °-0.13 Å °-0.0447 Å °0.0554 Å °0.0282 Å °-0.0825 Å °0.1118 Å °0.3045 Å °0.0061 Å °
Refinement TLS groupSelection: ALL

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