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- PDB-6f0p: Botulinum neurotoxin A4 Hc domain -

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Basic information

Entry
Database: PDB / ID: 6f0p
TitleBotulinum neurotoxin A4 Hc domain
ComponentsNeurotoxin type A
KeywordsTOXIN / botulinum neurotoxin A4 subtype / A4 / binding domain / Hc domain
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
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 ...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 / 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
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsDavies, J.R. / Rees, J. / 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
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54710
Polymers50,7571
Non-polymers7919
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint16 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.888, 115.888, 115.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Neurotoxin type A


Mass: 50756.523 Da / Num. of mol.: 1 / Fragment: Hc domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3LRX8

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Non-polymers , 5 types, 318 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4-Diaminobutane dihydrochloride, 10 mM D-L-Ornithine monohydrochloride, 0.1 M MOPSO/bis-tris pH 6.5, 15%(w/v) ...Details: 10 mM Spermine tetrahydrochloride, 10 mM Spermidine trihydrochloride, 10 mM 1,4-Diaminobutane dihydrochloride, 10 mM D-L-Ornithine monohydrochloride, 0.1 M MOPSO/bis-tris pH 6.5, 15%(w/v) PEG 3K, 20%(v/v) 1,2,4-butanetriol, 1%(w/v) NDSB 256

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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: Apr 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.34→81.95 Å / Num. obs: 116165 / % possible obs: 100 % / Redundancy: 21.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Net I/σ(I): 17.5
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 10.5 % / Rmerge(I) obs: 2.306 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5700 / CC1/2: 0.421 / Rpim(I) all: 0.74 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vua

2vua


Resolution: 1.34→81.95 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.603 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15829 2017 1.7 %RANDOM
Rwork0.14401 ---
obs0.14425 113786 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.807 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.34→81.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 49 309 3781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023623
X-RAY DIFFRACTIONr_bond_other_d0.0020.023334
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9434889
X-RAY DIFFRACTIONr_angle_other_deg0.91237734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92824.426183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67515654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1191523
X-RAY DIFFRACTIONr_chiral_restr0.2150.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02767
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_it2.9731.8061712
X-RAY DIFFRACTIONr_mcbond_other2.8721.8031711
X-RAY DIFFRACTIONr_mcangle_it4.0112.7242151
X-RAY DIFFRACTIONr_mcangle_other4.0122.7262152
X-RAY DIFFRACTIONr_scbond_it3.6782.1751911
X-RAY DIFFRACTIONr_scbond_other3.6782.1751911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6393.1132738
X-RAY DIFFRACTIONr_long_range_B_refined5.38122.134019
X-RAY DIFFRACTIONr_long_range_B_other5.3822.1334020
X-RAY DIFFRACTIONr_rigid_bond_restr1.56536957
X-RAY DIFFRACTIONr_sphericity_free22.3255207
X-RAY DIFFRACTIONr_sphericity_bonded12.90556989
LS refinement shellResolution: 1.34→1.375 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 131 -
Rwork0.266 8377 -
obs--99.96 %

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