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- PDB-8alp: Botulinum neurotoxin A6 cell binding domain crystal form II -

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Basic information

Entry
Database: PDB / ID: 8alp
TitleBotulinum neurotoxin A6 cell binding domain crystal form II
ComponentsBont/A1
KeywordsTOXIN / Botulinum neurotoxin / cell binding domain / hinge motion
Function / homology
Function and homology information


protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Bontoxilysin-A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2022
Title: Crystal Structures of the Clostridium botulinum Neurotoxin A6 Cell Binding Domain Alone and in Complex with GD1a Reveal Significant Conformational Flexibility.
Authors: Gregory, K.S. / Newell, A.R. / Mojanaga, O.O. / Liu, S.M. / Acharya, K.R.
History
DepositionAug 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Bont/A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2229
Polymers50,6821
Non-polymers5418
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint23 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.554, 78.938, 118.550
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 Bont/A1 / Botulinum neurotoxin type A


Mass: 50681.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C9WWY7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.83 Å3/Da / Density % sol: 32.63 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M magnesium acetate tetrahydrate, 0.1 M MES pH 6.5, 12% w/v of 50% PEG smear medium (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, ...Details: 0.1 M magnesium acetate tetrahydrate, 0.1 M MES pH 6.5, 12% w/v of 50% PEG smear medium (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→118.55 Å / Num. obs: 60147 / % possible obs: 99.6 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.023 / Net I/σ(I): 12
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 5.68 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2894 / CC1/2: 0.33 / Rpim(I) all: 1.125 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TWO

6two


Resolution: 1.5→65.705 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.286 / WRfactor Rwork: 0.246 / SU B: 2.573 / SU ML: 0.091 / Average fsc free: 0.8076 / Average fsc work: 0.8164 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2893 2990 4.979 %
Rwork0.2484 57057 -
all0.251 --
obs-60047 99.432 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.142 Å2
Baniso -1Baniso -2Baniso -3
1--0.442 Å20 Å20 Å2
2--1.803 Å2-0 Å2
3----1.362 Å2
Refinement stepCycle: LAST / Resolution: 1.5→65.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 35 124 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133213
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163137
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.6364306
X-RAY DIFFRACTIONr_angle_other_deg1.3551.5887180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5845374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24223.39177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95115594
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg2.91151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9781517
X-RAY DIFFRACTIONr_chiral_restr0.0680.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023592
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02794
X-RAY DIFFRACTIONr_nbd_refined0.1970.2574
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.23030
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21503
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21610
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2139
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.232
X-RAY DIFFRACTIONr_nbd_other0.2270.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.219
X-RAY DIFFRACTIONr_mcbond_it3.3313.5991517
X-RAY DIFFRACTIONr_mcbond_other3.3313.5991516
X-RAY DIFFRACTIONr_mcangle_it4.5625.3751884
X-RAY DIFFRACTIONr_mcangle_other4.5615.3751885
X-RAY DIFFRACTIONr_scbond_it3.9114.1071696
X-RAY DIFFRACTIONr_scbond_other3.914.1081697
X-RAY DIFFRACTIONr_scangle_it5.9475.9722422
X-RAY DIFFRACTIONr_scangle_other5.9465.9732423
X-RAY DIFFRACTIONr_lrange_it8.21942.8983529
X-RAY DIFFRACTIONr_lrange_other8.20342.8553520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.3581980.3741170.36944040.4620.46297.97910.369
1.539-1.5810.3462220.34140550.34143450.5430.55398.4350.336
1.581-1.6270.3222170.32138850.32141090.6550.65999.82960.313
1.627-1.6770.3551910.30938340.31140810.6930.71698.62780.294
1.677-1.7320.3252020.29137150.29339590.8080.80998.93910.27
1.732-1.7930.311750.25436020.25737870.8470.86899.73590.23
1.793-1.860.2871720.24234810.24436730.8880.89199.45550.217
1.86-1.9360.2811830.23333600.23635620.8830.90599.46660.209
1.936-2.0220.2531810.2232000.22233940.9070.92299.6170.2
2.022-2.1210.2711550.21831080.2232710.910.92299.75540.2
2.121-2.2350.2491690.20929650.21131400.9280.93299.80890.195
2.235-2.3710.2431310.21328050.21429380.9270.93699.93190.199
2.371-2.5340.2781370.23126560.23427940.9050.91799.96420.218
2.534-2.7370.271350.23124680.23326030.9130.9171000.221
2.737-2.9980.261310.23522670.23623980.9230.9261000.23
2.998-3.3510.277900.24320980.24421880.9040.9121000.245
3.351-3.8670.2741120.23118420.23419540.9130.9211000.243
3.867-4.7320.305880.24115800.24416680.8860.9161000.265
4.732-6.6750.361640.29612670.29913310.8630.8871000.327
6.675-65.7050.307370.2967530.2977920.9010.89499.74750.349

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