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- PDB-6twp: Binding domain of BoNT/A5 -

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Basic information

Entry
Database: PDB / ID: 6twp
TitleBinding domain of BoNT/A5
ComponentsBotulinum neurotoxin A5
KeywordsTOXIN / binding domain / botulinum neurotoxin
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion / protein transmembrane transporter activity / : / metalloendopeptidase activity / toxin activity / 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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Botulinum neurotoxin A5
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsDavies, J.R. / Acharya, K.R.
CitationJournal: Febs Open Bio / Year: 2020
Title: High-resolution crystal structures of the botulinum neurotoxin binding domains from subtypes A5 and A6.
Authors: Davies, J.R. / Britton, A. / Liu, S.M. / Acharya, K.R.
History
DepositionJan 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Botulinum neurotoxin A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7582
Polymers50,7221
Non-polymers351
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.547, 60.266, 185.147
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Botulinum neurotoxin A5 / Botulinum neurotoxin B / Botulinum neurotoxin subtype A5


Mass: 50722.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MLZ was modelled instead of a lysine following inspection of the electron density.
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont/A5, boNT / Plasmid: pJ401 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C7BEA8
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Sodium potassium tartrate tetrahydrate, 0.1 M Sodium oxamate, 0.1 M Imidazole, 0.1 M 2-[N- ...Details: 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Sodium potassium tartrate tetrahydrate, 0.1 M Sodium oxamate, 0.1 M Imidazole, 0.1 M 2-[N-morpholino]ethanesulfonic acid, pH 6.5, 10% v/v Ethylene glycol, 10% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.15→92.57 Å / Num. obs: 173797 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.998 / Net I/σ(I): 11.9
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 84519 / CC1/2: 0.447 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VUA

2vua


Resolution: 1.15→92.57 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.228 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1612 3494 2.014 %
Rwork0.1351 --
all0.136 --
obs-173516 99.881 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 16.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.259 Å20 Å20 Å2
2---1.65 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.15→92.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 1 509 3926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0133945
X-RAY DIFFRACTIONr_bond_other_d0.0060.0173554
X-RAY DIFFRACTIONr_angle_refined_deg2.2021.6315395
X-RAY DIFFRACTIONr_angle_other_deg1.6261.5798319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6065504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71824.105229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20715723
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg8.231151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3861519
X-RAY DIFFRACTIONr_chiral_restr0.1250.2510
X-RAY DIFFRACTIONr_chiral_restr_other0.3480.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024597
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02848
X-RAY DIFFRACTIONr_nbd_refined0.2850.2701
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.23463
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21802
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21867
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2640.2358
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2120.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.220
X-RAY DIFFRACTIONr_nbd_other0.1860.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.239
X-RAY DIFFRACTIONr_mcbond_it1.9561.4461881
X-RAY DIFFRACTIONr_mcbond_other1.9231.4441880
X-RAY DIFFRACTIONr_mcangle_it2.4742.1772408
X-RAY DIFFRACTIONr_mcangle_other2.4772.1792409
X-RAY DIFFRACTIONr_scbond_it3.791.7492064
X-RAY DIFFRACTIONr_scbond_other3.7881.7482064
X-RAY DIFFRACTIONr_scangle_it4.2862.5172978
X-RAY DIFFRACTIONr_scangle_other4.2852.5192979
X-RAY DIFFRACTIONr_lrange_it4.28518.8584580
X-RAY DIFFRACTIONr_lrange_other4.01218.0134453
X-RAY DIFFRACTIONr_rigid_bond_restr6.02737499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.2252280.22812460X-RAY DIFFRACTION99.5528
1.18-1.2120.2282340.20412122X-RAY DIFFRACTION99.7739
1.212-1.2470.1952540.18811770X-RAY DIFFRACTION99.8008
1.247-1.2860.1822190.16711492X-RAY DIFFRACTION99.8636
1.286-1.3280.1882390.15511105X-RAY DIFFRACTION99.8679
1.328-1.3740.1662260.14310765X-RAY DIFFRACTION99.8819
1.374-1.4260.172180.12910372X-RAY DIFFRACTION99.9245
1.426-1.4850.1542160.11210024X-RAY DIFFRACTION99.9219
1.485-1.5510.1322090.1019645X-RAY DIFFRACTION99.8682
1.551-1.6260.1451920.0989199X-RAY DIFFRACTION99.9681
1.626-1.7140.1271730.0898765X-RAY DIFFRACTION99.9441
1.714-1.8180.1271710.0928355X-RAY DIFFRACTION99.9883
1.818-1.9440.1391700.1027816X-RAY DIFFRACTION99.9499
1.944-2.0990.1431630.1127293X-RAY DIFFRACTION99.9598
2.099-2.2990.1291390.1176783X-RAY DIFFRACTION99.9567
2.299-2.5710.1651270.1226153X-RAY DIFFRACTION99.9841
2.571-2.9680.1841140.1395433X-RAY DIFFRACTION100
2.968-3.6340.157890.154665X-RAY DIFFRACTION100
3.634-5.1350.164720.1433660X-RAY DIFFRACTION99.9732
5.135-92.570.232420.2292145X-RAY DIFFRACTION99.9086

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