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- PDB-6g8v: Crystal structure of the light chain of botulinum neurotoxin X (r... -

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Basic information

Entry
Database: PDB / ID: 6g8v
TitleCrystal structure of the light chain of botulinum neurotoxin X (residues 2-442)
ComponentsLight chain of botulinum neurotoxin X (res. 2-442)
KeywordsTOXIN / neurotoxin / endopeptidase
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / 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, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin type X
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWu, Y. / Kammerer, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163449 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the light chain of botulinum neurotoxin X (residues 2-442)
Authors: Wu, Y. / Kammerer, R.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light chain of botulinum neurotoxin X (res. 2-442)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6096
Polymers52,1751
Non-polymers4345
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-38 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.320, 87.260, 93.850
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 Light chain of botulinum neurotoxin X (res. 2-442)


Mass: 52174.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DPK1*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES 10% w/v PEG 6000 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 1.45→41.328 Å / Num. obs: 88274 / % possible obs: 99.86 % / Redundancy: 13.3 % / Biso Wilson estimate: 22.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07576 / Rpim(I) all: 0.02165 / Rrim(I) all: 0.07888 / Net I/σ(I): 18.51
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.994 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8719 / CC1/2: 0.424 / Rpim(I) all: 0.8365 / Rrim(I) all: 3.111 / % possible all: 99.89

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QIZ

3qiz


Resolution: 1.45→41.328 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.54
RfactorNum. reflection% reflection
Rfree0.1824 4414 5 %
Rwork0.1438 --
obs0.1457 88257 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→41.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 25 435 3851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013584
X-RAY DIFFRACTIONf_angle_d0.8914873
X-RAY DIFFRACTIONf_dihedral_angle_d13.2361370
X-RAY DIFFRACTIONf_chiral_restr0.08550
X-RAY DIFFRACTIONf_plane_restr0.007635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.62151460.56152775X-RAY DIFFRACTION100
1.4665-1.48370.461440.40572725X-RAY DIFFRACTION100
1.4837-1.50180.38591460.33252783X-RAY DIFFRACTION100
1.5018-1.52080.32041450.29772753X-RAY DIFFRACTION100
1.5208-1.54090.35741460.26822781X-RAY DIFFRACTION100
1.5409-1.5620.30381470.23772781X-RAY DIFFRACTION100
1.562-1.58430.2791450.22482754X-RAY DIFFRACTION100
1.5843-1.60790.24051450.20382761X-RAY DIFFRACTION100
1.6079-1.6330.2831450.20022757X-RAY DIFFRACTION100
1.633-1.65980.23381450.19432754X-RAY DIFFRACTION100
1.6598-1.68840.22531460.17812778X-RAY DIFFRACTION100
1.6884-1.71910.19491460.13822769X-RAY DIFFRACTION100
1.7191-1.75220.19221460.12362778X-RAY DIFFRACTION100
1.7522-1.7880.19061470.11472776X-RAY DIFFRACTION100
1.788-1.82690.18891460.11472792X-RAY DIFFRACTION100
1.8269-1.86940.15911460.11392766X-RAY DIFFRACTION100
1.8694-1.91610.15861470.1112796X-RAY DIFFRACTION100
1.9161-1.96790.17021460.11642768X-RAY DIFFRACTION100
1.9679-2.02580.15921470.11552784X-RAY DIFFRACTION100
2.0258-2.09120.15461480.11632817X-RAY DIFFRACTION100
2.0912-2.16590.18151460.11912781X-RAY DIFFRACTION100
2.1659-2.25270.16551480.11882806X-RAY DIFFRACTION100
2.2527-2.35520.15651470.11282803X-RAY DIFFRACTION100
2.3552-2.47930.14111480.1182802X-RAY DIFFRACTION100
2.4793-2.63460.17291480.12682810X-RAY DIFFRACTION100
2.6346-2.8380.15111490.1342833X-RAY DIFFRACTION100
2.838-3.12350.17941500.13712844X-RAY DIFFRACTION100
3.1235-3.57530.16641480.13712820X-RAY DIFFRACTION99
3.5753-4.50360.16711510.13162876X-RAY DIFFRACTION100
4.5036-41.3450.19361600.17583020X-RAY DIFFRACTION100

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