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- PDB-8hkh: Crystal structure of the LC/A1-DARPin18 complex -

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Basic information

Entry
Database: PDB / ID: 8hkh
TitleCrystal structure of the LC/A1-DARPin18 complex
Components
  • BoNT/A
  • Designed ankyrin repeat protein 18
KeywordsTOXIN / Botulinum Neurotoxin / DARPin / Catalytic Domain
Function / homology
Function and homology information


bontoxilysin / 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
Biological speciesClostridium botulinum (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWu, Y. / Leka, O. / Kammerer, R.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163449 Switzerland
Swiss National Science Foundation31003A_170028 Switzerland
CitationJournal: To Be Published
Title: A DARPin Increases the Catalytic Activity of BoNT/A1
Authors: Leka, O. / Wu, Y. / Kammerer, R. / Li, X. / Plueckthun, A.
History
DepositionNov 26, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BoNT/A
B: BoNT/A
C: Designed ankyrin repeat protein 18
D: Designed ankyrin repeat protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7186
Polymers132,5874
Non-polymers1312
Water46826
1
A: BoNT/A
C: Designed ankyrin repeat protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3593
Polymers66,2942
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BoNT/A
D: Designed ankyrin repeat protein 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3593
Polymers66,2942
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.560, 59.630, 102.180
Angle α, β, γ (deg.)74.980, 89.900, 73.150
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRchain AAA1 - 42016 - 435
21SERSERTHRTHRchain BBB1 - 42016 - 435
12HISHISLEULEUchain CCC7 - 1407 - 140
22HISHISLEULEUchain DDD7 - 1407 - 140

NCS ensembles :
ID
1
2

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Components

#1: Protein BoNT/A


Mass: 49952.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: a / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q7B8V4
#2: Protein Designed ankyrin repeat protein 18 / DARPin18


Mass: 16341.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli K-12 (bacteria)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5 28 % w/v Jeffamine ED-2003

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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 EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→49.19 Å / Num. obs: 39460 / % possible obs: 93.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.03 Å2 / CC1/2: 0.976 / Net I/σ(I): 4.49
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.17 / Num. unique obs: 2962 / CC1/2: 0.452 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.188 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 36.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3061 1659 5 %
Rwork0.2617 31514 -
obs0.2639 33173 93.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.21 Å2 / Biso mean: 52.3634 Å2 / Biso min: 18.52 Å2
Refinement stepCycle: final / Resolution: 2.7→49.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8840 0 2 26 8868
Biso mean--42.38 31.97 -
Num. residues----1108
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4046X-RAY DIFFRACTION7.141TORSIONAL
12B4046X-RAY DIFFRACTION7.141TORSIONAL
21C1216X-RAY DIFFRACTION7.141TORSIONAL
22D1216X-RAY DIFFRACTION7.141TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.77950.41291400.3296267095
2.7795-2.86920.43811410.3313266295
2.8692-2.97170.38171420.3243270094
2.9717-3.09070.37871380.3349261893
3.0907-3.23130.37651370.352261293
3.2313-3.40160.45021360.3433257191
3.4016-3.61470.35351280.3088243787
3.6147-3.89370.32161330.2668252889
3.8937-4.28530.27121450.2147273997
4.2853-4.90490.21131420.2048271396
4.9049-6.17780.25691390.2249265294
6.1778-49.1880.22781380.2096261293

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