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- PDB-8agk: Botulinum neurotoxin subtype A6 cell binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8agk
TitleBotulinum neurotoxin subtype A6 cell binding domain in complex with GD1a ganglioside
ComponentsBont/A1
KeywordsTOXIN / Botulism / ganglioside / botulinum neurotoxin / cell binding domain / complex / subtype
Function / homology
Function and homology information


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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Bont/A1
Similarity search - Component
Biological speciesClostridium botulinum str. Iwanei E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M. / Newell, A.R. / Mojanaga, O.O.
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
DepositionJul 20, 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)52,30910
Polymers50,6821
Non-polymers1,6289
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.307, 83.636, 58.313
Angle α, β, γ (deg.)90.000, 98.659, 90.000
Int Tables number4
Space group name H-MP1211

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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 str. Iwanei E (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C9WWY7
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-alpha-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4DGalpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,5,4/[a2122h-1a_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4-5/a4-b1_b4-c1_c3-d1_d3-e2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Galp]{[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / Details: 0.2 M NaCl, 0.1 M HEPES pH 7.0, 20% w/v PEG 6000

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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 X 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→57.65 Å / Num. obs: 67218 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rpim(I) all: 0.05 / Net I/σ(I): 7.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 3357 / CC1/2: 0.991 / Rpim(I) all: 2.241 / % possible all: 100

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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→57.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.207 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 3343 4.978 %0.05
Rwork0.2033 63813 --
all0.205 ---
obs-67156 99.949 %-
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: 27.134 Å2
Baniso -1Baniso -2Baniso -3
1--0.885 Å2-0 Å20.47 Å2
2---0.714 Å2-0 Å2
3---1.391 Å2
Refinement stepCycle: LAST / Resolution: 1.5→57.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 114 197 3713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133608
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163442
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6554855
X-RAY DIFFRACTIONr_angle_other_deg1.3421.6027904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6325418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80323.553197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75515642
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7681517
X-RAY DIFFRACTIONr_chiral_restr0.0740.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
X-RAY DIFFRACTIONr_nbd_refined0.1910.2552
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23240
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21727
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2179
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.218
X-RAY DIFFRACTIONr_nbd_other0.1970.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.210
X-RAY DIFFRACTIONr_mcbond_it2.1952.5381663
X-RAY DIFFRACTIONr_mcbond_other2.1882.5361662
X-RAY DIFFRACTIONr_mcangle_it3.1813.7872075
X-RAY DIFFRACTIONr_mcangle_other3.1813.7912076
X-RAY DIFFRACTIONr_scbond_it3.2873.0321945
X-RAY DIFFRACTIONr_scbond_other3.2873.0321945
X-RAY DIFFRACTIONr_scangle_it5.0044.3672777
X-RAY DIFFRACTIONr_scangle_other5.0034.3682778
X-RAY DIFFRACTIONr_lrange_it6.37830.2023906
X-RAY DIFFRACTIONr_lrange_other6.35830.0733881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.4432370.4244758X-RAY DIFFRACTION99.98
1.539-1.5810.3882290.3864588X-RAY DIFFRACTION99.9585
1.581-1.6270.3892540.3774387X-RAY DIFFRACTION99.8924
1.627-1.6770.3642330.3354324X-RAY DIFFRACTION99.9123
1.677-1.7320.3392090.3164202X-RAY DIFFRACTION99.9547
1.732-1.7930.2941860.2914111X-RAY DIFFRACTION99.8606
1.793-1.860.2962050.2643903X-RAY DIFFRACTION99.9027
1.86-1.9360.2551830.2283806X-RAY DIFFRACTION99.8998
1.936-2.0220.2191880.23620X-RAY DIFFRACTION99.9475
2.022-2.1210.2191610.183489X-RAY DIFFRACTION99.9726
2.121-2.2350.2251680.1813285X-RAY DIFFRACTION99.971
2.235-2.3710.1981780.1783094X-RAY DIFFRACTION100
2.371-2.5340.251860.1832912X-RAY DIFFRACTION100
2.534-2.7360.2481490.1852722X-RAY DIFFRACTION100
2.736-2.9970.2211170.1822539X-RAY DIFFRACTION100
2.997-3.350.2261470.1672255X-RAY DIFFRACTION100
3.35-3.8660.2011000.1572014X-RAY DIFFRACTION100
3.866-4.7290.161010.141712X-RAY DIFFRACTION100
4.729-6.6650.222670.1741339X-RAY DIFFRACTION100
6.665-57.650.207450.177753X-RAY DIFFRACTION99.75

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