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- PDB-5mk8: Crystal structure of the receptor-binding domain of the FA hybrid... -

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Basic information

Entry
Database: PDB / ID: 5mk8
TitleCrystal structure of the receptor-binding domain of the FA hybrid Clostridium botulinum neurotoxin
ComponentsBotulinum neurotoxin FA binding domain
KeywordsTOXIN / bacterial toxin Toxin receptor binding domain jelly roll fold beta trefoil fold
Function / homology
Function and homology information


Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Neurotoxin heavy chain 18 kDa fragment
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDavies, J.R. / Acharya, K.R.
CitationJournal: PeerJ / Year: 2018
Title: High resolution crystal structures of the receptor-binding domain ofClostridium botulinumneurotoxin serotypes A and FA.
Authors: Davies, J.R. / Hackett, G.S. / Liu, S.M. / Acharya, K.R.
History
DepositionDec 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Botulinum neurotoxin FA binding domain
B: Botulinum neurotoxin FA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,55717
Polymers101,9092
Non-polymers64815
Water10,971609
1
A: Botulinum neurotoxin FA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3029
Polymers50,9551
Non-polymers3478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Botulinum neurotoxin FA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2568
Polymers50,9551
Non-polymers3017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.009, 118.009, 173.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein Botulinum neurotoxin FA binding domain


Mass: 50954.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein sequence matches genbank KGO15617.1 from residue 859 onward.
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R540*PLUS
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 4 M sodium formate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→118.009 Å / Num. obs: 89871 / % possible obs: 100 % / Redundancy: 26 % / CC1/2: 0.999 / Net I/σ(I): 12.6
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 23.7 % / Mean I/σ(I) obs: 2.3 / CC1/2: 0.832 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→118.009 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.2117 4504 5.01 %
Rwork0.1792 --
obs0.1808 89848 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→118.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6886 0 37 609 7532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077075
X-RAY DIFFRACTIONf_angle_d0.8789540
X-RAY DIFFRACTIONf_dihedral_angle_d14.7454221
X-RAY DIFFRACTIONf_chiral_restr0.0611016
X-RAY DIFFRACTIONf_plane_restr0.0041224

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