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- PDB-7dvl: Crystal Structure of the Catalytic Domain of Botulinum Neurotoxin... -

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Basic information

Entry
Database: PDB / ID: 7dvl
TitleCrystal Structure of the Catalytic Domain of Botulinum Neurotoxin Subtype A3
ComponentsBont/A3
KeywordsTOXIN / Botulinum Neurotoxin / Catalytic Domain / activity / stability
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
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 Å
AuthorsWu, Y. / Leka, O. / Kammerer, R. / Li, X.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163449 Switzerland
Swiss National Science Foundation31003A_170028 Switzerland
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Crystal structure of the catalytic domain of botulinum neurotoxin subtype A3.
Authors: Leka, O. / Wu, Y. / Li, X. / Kammerer, R.A.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 2023Group: 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: Bont/A3
B: Bont/A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0794
Polymers94,9492
Non-polymers1312
Water9,404522
1
A: Bont/A3
hetero molecules

B: Bont/A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0794
Polymers94,9492
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+3/2,-y+1,z+1/21
Buried area2610 Å2
ΔGint-83 kcal/mol
Surface area35280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.250, 97.420, 141.250
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 Bont/A3 / Botulinum neurotoxin type A


Mass: 47474.309 Da / Num. of mol.: 2 / Mutation: E226Q, Y368F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont, FDC09_07905 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: D3IV24
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 48.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M proline, 0.1 M HEPES pH 7.5, 10 %w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.006→48.7243 Å / Num. obs: 61562 / % possible obs: 96.61 % / Redundancy: 10.8 % / Biso Wilson estimate: 24.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1431 / Rpim(I) all: 0.04581 / Rrim(I) all: 0.1505 / Net I/σ(I): 13.26
Reflection shellResolution: 2.006→2.078 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 6025 / CC1/2: 0.675 / Rpim(I) all: 0.3247 / Rrim(I) all: 1.098 / % possible all: 98.58

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTG

1xtg


Resolution: 2.006→48.71 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 2993 5 %
Rwork0.2049 --
obs0.2063 59871 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.006→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 2 522 7062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036712
X-RAY DIFFRACTIONf_angle_d0.6399096
X-RAY DIFFRACTIONf_dihedral_angle_d10.1863982
X-RAY DIFFRACTIONf_chiral_restr0.046985
X-RAY DIFFRACTIONf_plane_restr0.0041193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.006-2.03890.31361400.25062667X-RAY DIFFRACTION97
2.0389-2.07410.28761470.25042784X-RAY DIFFRACTION100
2.0741-2.11180.24611450.22812751X-RAY DIFFRACTION100
2.1118-2.15240.2751450.23042751X-RAY DIFFRACTION100
2.1524-2.19630.31631450.28532773X-RAY DIFFRACTION100
2.1963-2.24410.52381020.52571996X-RAY DIFFRACTION72
2.2441-2.29630.56981050.53471951X-RAY DIFFRACTION71
2.2963-2.35370.28141480.24432806X-RAY DIFFRACTION100
2.3537-2.41740.21711440.18962749X-RAY DIFFRACTION100
2.4174-2.48850.24211450.19142759X-RAY DIFFRACTION99
2.4885-2.56880.25391460.18852755X-RAY DIFFRACTION99
2.5688-2.66060.26671420.18652704X-RAY DIFFRACTION97
2.6606-2.76710.23771470.1972797X-RAY DIFFRACTION100
2.7671-2.89310.24421480.19332806X-RAY DIFFRACTION100
2.8931-3.04560.20621460.18712785X-RAY DIFFRACTION100
3.0456-3.23640.20081480.19432809X-RAY DIFFRACTION100
3.2364-3.48620.21531490.19332832X-RAY DIFFRACTION100
3.4862-3.83690.22151450.1942748X-RAY DIFFRACTION98
3.8369-4.39180.17171490.15432832X-RAY DIFFRACTION99
4.3918-5.53190.16021480.14092808X-RAY DIFFRACTION98
5.5319-48.710.18251590.18093015X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6908-0.09350.62782.4809-1.10045.3247-0.02360.19990.0986-0.10650.12050.1065-0.4204-0.1153-0.05160.2255-0.01590.00220.16670.00330.229757.521275.406853.4258
24.12794.1047-0.4585.0646-0.74810.1617-0.33581.1395-0.404-0.61770.21990.62640.8829-0.8321-0.03880.5032-0.2054-0.14210.6109-0.08650.462745.485758.056547.3757
32.52810.6630.81932.802-0.0522.6343-0.14850.11010.1566-0.15030.05060.50670.0224-0.35160.10960.17130.01280.01530.2342-0.01460.202247.263766.925760.2929
42.02310.0545-0.78551.6676-0.63861.9169-0.15280.30290.0392-0.29310.0689-0.13250.0168-0.04050.0780.263-0.04660.00550.1763-0.0450.185666.45866.420951.9424
53.5888-0.9379-1.65750.91460.13892.35360.04190.307-0.1218-0.1869-0.00840.11990.0655-0.19450.07170.1971-0.0401-0.05120.163-0.05290.207357.64657.013758.3319
61.5940.2484-0.4471.7549-0.1151.88890.08340.1299-0.3757-0.2176-0.01040.1390.2641-0.248-0.03160.2053-0.0299-0.03820.1923-0.01460.222858.04946.502761.5222
72.32681.7214-0.19783.8586-0.76751.2928-0.05070.0711-0.1661-0.12560.0467-0.37790.10780.17770.02280.21960.02310.01120.2083-0.04280.23977.389655.201159.2576
86.03870.0288-2.09012.1582-0.30321.9937-0.0615-0.014-0.28010.1375-0.0101-0.0573-0.02440.07070.04910.24130.0065-0.02830.1791-0.02310.242669.985554.992970.9328
92.2568-0.75620.84751.5795-0.92912.1603-0.0526-0.0317-0.3219-0.03180.03820.25770.2309-0.0817-0.04630.228-0.00190.07840.2322-0.01250.263248.183460.625572.2545
105.18721.47713.59382.23752.13853.26690.0764-0.0958-0.1910.3258-0.0330.3060.4358-0.45010.06870.2334-0.03190.05660.25660.00730.341740.565760.840375.3778
112.4974-0.63930.67511.79220.18311.0972-0.1377-0.08020.21130.02220.0337-0.0167-0.194-0.08070.12210.2750.01230.01540.1901-0.00340.184844.362780.911626.4232
122.7216-0.2257-0.36441.4936-0.4761.2844-0.09420.11370.0745-0.00460.0270.0153-0.1235-0.0330.06460.21230.00370.02060.1502-0.00550.161744.596376.907219.7491
131.42250.38391.08660.84140.38062.2177-0.04250.3263-0.0643-0.14140.08010.03010.00360.3022-0.02410.20790.00070.03230.1830.00550.232751.745365.04089.7779
142.3799-0.53640.25551.18780.01581.10220.0213-0.1452-0.30690.1546-0.02820.16710.0664-0.03530.00560.2380.00420.05220.14980.04620.215144.496965.047323.9395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 102 )
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 165 )
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 218 )
6X-RAY DIFFRACTION6chain 'A' and (resid 219 through 257 )
7X-RAY DIFFRACTION7chain 'A' and (resid 258 through 336 )
8X-RAY DIFFRACTION8chain 'A' and (resid 337 through 359 )
9X-RAY DIFFRACTION9chain 'A' and (resid 360 through 392 )
10X-RAY DIFFRACTION10chain 'A' and (resid 393 through 418 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 140 )
12X-RAY DIFFRACTION12chain 'B' and (resid 141 through 218 )
13X-RAY DIFFRACTION13chain 'B' and (resid 219 through 301 )
14X-RAY DIFFRACTION14chain 'B' and (resid 302 through 418 )

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