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- PDB-6f47: Crystal structure of the catalytic domain of botulinum neurotoxin X -

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Basic information

Entry
Database: PDB / ID: 6f47
TitleCrystal structure of the catalytic domain of botulinum neurotoxin X
ComponentsCatalytic domain of botulinum neurotoxin X
KeywordsTOXIN / botulinum neurotoxin / botulinum toxin / zinc endopeptidase
Function / homologyClostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / metalloendopeptidase activity / proteolysis / zinc ion binding / Catalytic domain of botulinum neurotoxin X
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMasuyer, G. / Henriksson, L. / Kosenina, S. / Zhang, S. / Barkho, S. / Shen, Y. / Dong, M. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2014-5667 Sweden
CitationJournal: Sci Rep / Year: 2018
Title: Structural characterisation of the catalytic domain of botulinum neurotoxin X - high activity and unique substrate specificity.
Authors: Masuyer, G. / Zhang, S. / Barkho, S. / Shen, Y. / Henriksson, L. / Kosenina, S. / Dong, M. / Stenmark, P.
History
DepositionNov 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Database references / Category: citation
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
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Catalytic domain of botulinum neurotoxin X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1792
Polymers52,1141
Non-polymers651
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.340, 86.732, 93.079
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 Catalytic domain of botulinum neurotoxin X


Mass: 52113.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant Light Chain (catalytic domain) of botulinum neurotoxin X
Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: 111 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A384E149*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG1500, MMT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.35→63.45 Å / Num. obs: 98954 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.053 / Rrim(I) all: 0.098 / Net I/σ(I): 9.2
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 1 / Num. unique obs: 3303 / CC1/2: 0.417 / Rpim(I) all: 0.738 / Rrim(I) all: 1.23 / % possible all: 64.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1epw

1epw


Resolution: 1.35→63.45 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.541 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17617 4986 5 %RANDOM
Rwork0.14291 ---
obs0.14458 93863 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.599 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20 Å2
2---1.01 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.35→63.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 1 565 3879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023436
X-RAY DIFFRACTIONr_bond_other_d0.0020.023147
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9684683
X-RAY DIFFRACTIONr_angle_other_deg0.93537367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6975435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89525.689167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95615604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5661512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213847
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02657
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5121.8211681
X-RAY DIFFRACTIONr_mcbond_other1.5121.8191680
X-RAY DIFFRACTIONr_mcangle_it1.8542.7412108
X-RAY DIFFRACTIONr_mcangle_other1.8542.7422109
X-RAY DIFFRACTIONr_scbond_it1.852.0771755
X-RAY DIFFRACTIONr_scbond_other1.852.0771755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2223.0052566
X-RAY DIFFRACTIONr_long_range_B_refined4.02524.134166
X-RAY DIFFRACTIONr_long_range_B_other3.23722.633975
X-RAY DIFFRACTIONr_rigid_bond_restr1.41836583
X-RAY DIFFRACTIONr_sphericity_free29.3975305
X-RAY DIFFRACTIONr_sphericity_bonded9.93956762
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 235 -
Rwork0.357 4802 -
obs--65.93 %

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