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- PDB-6g8u: Crystal structure of the light chain of botulinum neurotoxin X (r... -

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Basic information

Entry
Database: PDB / ID: 6g8u
TitleCrystal structure of the light chain of botulinum neurotoxin X (residues 2-427)
ComponentsLight chain of botulinum neurotoxin X (res. 2-427)
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 C-terminal / Clostridium neurotoxin, receptor binding N-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: 1.308 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 2-427)
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. 2-427)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3972
Polymers50,3321
Non-polymers651
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.600, 86.950, 93.390
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. 2-427)


Mass: 50331.773 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES 10% w/v PEG 8000 8% v/v Ethylene glycol pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000041 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000041 Å / Relative weight: 1
ReflectionResolution: 1.308→43.11 Å / Num. obs: 115320 / % possible obs: 99.75 % / Redundancy: 13.1 % / Biso Wilson estimate: 17.89 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07264 / Rpim(I) all: 0.02087 / Rrim(I) all: 0.07565 / Net I/σ(I): 18.36
Reflection shellResolution: 1.308→1.355 Å / Redundancy: 13 % / Rmerge(I) obs: 2.878 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 11237 / CC1/2: 0.493 / Rpim(I) all: 0.8238 / Rrim(I) all: 2.996 / % possible all: 98.24

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QIZ

3qiz


Resolution: 1.308→43.11 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.49
RfactorNum. reflection% reflection
Rfree0.169 5764 5 %
Rwork0.1493 --
obs0.1503 115280 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.308→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 1 479 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073475
X-RAY DIFFRACTIONf_angle_d0.9494733
X-RAY DIFFRACTIONf_dihedral_angle_d13.2931332
X-RAY DIFFRACTIONf_chiral_restr0.077532
X-RAY DIFFRACTIONf_plane_restr0.007623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3081-1.3230.47331800.45533411X-RAY DIFFRACTION95
1.323-1.33850.35591920.3613653X-RAY DIFFRACTION100
1.3385-1.35490.34411900.32013604X-RAY DIFFRACTION100
1.3549-1.3720.33241900.28933609X-RAY DIFFRACTION100
1.372-1.39010.31471910.26953630X-RAY DIFFRACTION100
1.3901-1.40910.27511890.24253591X-RAY DIFFRACTION100
1.4091-1.42920.25341920.21833652X-RAY DIFFRACTION100
1.4292-1.45060.24871900.19773613X-RAY DIFFRACTION100
1.4506-1.47330.19011890.17463607X-RAY DIFFRACTION100
1.4733-1.49740.18221920.1543632X-RAY DIFFRACTION100
1.4974-1.52320.22141890.13893601X-RAY DIFFRACTION100
1.5232-1.55090.20111910.13543646X-RAY DIFFRACTION100
1.5509-1.58080.1681920.12733645X-RAY DIFFRACTION100
1.5808-1.6130.15961910.1163626X-RAY DIFFRACTION100
1.613-1.64810.1521910.11773624X-RAY DIFFRACTION100
1.6481-1.68640.17861910.11523629X-RAY DIFFRACTION100
1.6864-1.72860.16171930.11273668X-RAY DIFFRACTION100
1.7286-1.77540.14021920.1143643X-RAY DIFFRACTION100
1.7754-1.82760.15211910.11993640X-RAY DIFFRACTION100
1.8276-1.88660.14431910.12013627X-RAY DIFFRACTION100
1.8866-1.9540.14681930.12513669X-RAY DIFFRACTION100
1.954-2.03230.16091930.12543670X-RAY DIFFRACTION100
2.0323-2.12480.16131930.12423661X-RAY DIFFRACTION100
2.1248-2.23680.14241940.12373682X-RAY DIFFRACTION100
2.2368-2.37690.13261930.12443664X-RAY DIFFRACTION100
2.3769-2.56040.15361950.13453709X-RAY DIFFRACTION100
2.5604-2.81810.16751950.14443704X-RAY DIFFRACTION100
2.8181-3.22580.15031960.15133727X-RAY DIFFRACTION100
3.2258-4.06390.15981970.15013749X-RAY DIFFRACTION100
4.0639-49.67310.17592080.16933930X-RAY DIFFRACTION100

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