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- PDB-6f0o: Botulinum neurotoxin A3 Hc domain -

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Basic information

Entry
Database: PDB / ID: 6f0o
TitleBotulinum neurotoxin A3 Hc domain
ComponentsBontoxilysin A
KeywordsTOXIN / botulinum neurotoxin A3 subtype / A3 / binding domain / Hc domain
Function / homology
Function and homology information


bontoxilysin / negative regulation of neurotransmitter secretion / protein transmembrane transporter activity / : / metalloendopeptidase activity / toxin activity / zinc ion binding / extracellular region
Similarity search - Function
Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, N-terminal receptor binding / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, receptor-binding C-terminal / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, N-terminal receptor binding / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, receptor-binding C-terminal / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROPANOIC ACID / Bontoxilysin A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDavies, J.R. / Liu, S.M. / Acharya, K.R.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: High resolution crystal structures of Clostridium botulinum neurotoxin A3 and A4 binding domains.
Authors: Davies, J.R. / Rees, J. / Liu, S.M. / Acharya, K.R.
History
DepositionNov 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bontoxilysin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8394
Polymers50,4641
Non-polymers3743
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint4 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.757, 96.474, 110.979
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 Bontoxilysin A


Mass: 50464.461 Da / Num. of mol.: 1 / Fragment: Hc domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (strain Loch Maree / Type A3) (bacteria)
Gene: botA, CLK_A0076 / Production host: Escherichia coli (E. coli) / References: UniProt: B1L2G5, bontoxilysin
#2: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MIB pH 4.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→96.47 Å / Num. obs: 55445 / % possible obs: 96.9 % / Redundancy: 12.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.036 / Net I/σ(I): 10.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2169 / CC1/2: 0.639 / Rpim(I) all: 0.639 / % possible all: 79.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vua
Resolution: 1.6→72.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.892 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21444 1948 3.5 %RANDOM
Rwork0.17926 ---
obs0.18045 53416 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0 Å2
2--0.78 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.6→72.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 25 364 3708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023407
X-RAY DIFFRACTIONr_bond_other_d0.0020.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9484592
X-RAY DIFFRACTIONr_angle_other_deg1.01337264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86425.119168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35115613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.421514
X-RAY DIFFRACTIONr_chiral_restr0.1090.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
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_it1.9682.1331623
X-RAY DIFFRACTIONr_mcbond_other1.9642.1311622
X-RAY DIFFRACTIONr_mcangle_it2.9413.182020
X-RAY DIFFRACTIONr_mcangle_other2.943.1822021
X-RAY DIFFRACTIONr_scbond_it2.882.4641784
X-RAY DIFFRACTIONr_scbond_other2.882.4641784
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4293.5532573
X-RAY DIFFRACTIONr_long_range_B_refined6.13425.9723866
X-RAY DIFFRACTIONr_long_range_B_other6.13325.9793867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 111 -
Rwork0.249 3307 -
obs--82.2 %

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