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- PDB-9gy5: Crystal structure of the catalytic domain from the BoNT-like toxi... -

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Entry
Database: PDB / ID: 9gy5
TitleCrystal structure of the catalytic domain from the BoNT-like toxin complex PG1 of Paeniclostridium ghonii
ComponentsCatalytic domain from the BoNT-like toxin complex PG1 of Paeniclostridium ghonii
KeywordsTOXIN / neurotoxin / metalloprotease
Function / homologyACETATE ION
Function and homology information
Biological speciesParaclostridium ghonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMasuyer, G. / Stenmark, P.
Funding support Sweden, Denmark, 3items
OrganizationGrant numberCountry
Swedish Research Council2022-03681 Sweden
Cancerfonden20 1287 PjF Sweden
Novo Nordisk FoundationNNF20OC0064789 Denmark
CitationJournal: To Be Published
Title: Structures of BoNT-like toxin complexes Paeniclostridium ghonii
Authors: Masuyer, G. / Stenmark, P. / Dong, M.
History
DepositionOct 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Catalytic domain from the BoNT-like toxin complex PG1 of Paeniclostridium ghonii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2918
Polymers44,6901
Non-polymers6017
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-85 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.217, 79.217, 274.532
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Catalytic domain from the BoNT-like toxin complex PG1 of Paeniclostridium ghonii


Mass: 44690.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Recombinant protein with first two residues from expression vector. Disordered regions not included in the structure (one loop and C-ter). Note protein is not in Uniprot yet - see NCBI entry WP_250673407
Source: (gene. exp.) Paraclostridium ghonii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: bontoxilysin

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Non-polymers , 5 types, 173 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0 5% v/v Tacsimate TM pH 7.0 10% w/v Polyethylene glycol monomethyl ether 5,000
Temp details: room temp

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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: Jan 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→61.37 Å / Num. obs: 48514 / % possible obs: 100 % / Redundancy: 37.9 % / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.035 / Rrim(I) all: 0.16 / Net I/σ(I): 14.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 39 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2788 / CC1/2: 0.492 / Rpim(I) all: 2.72 / Rrim(I) all: 12.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→54.952 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.963 / SU B: 10.298 / SU ML: 0.138 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2504 2430 5.035 %
Rwork0.2215 45834 -
all0.223 --
obs-48264 99.68 %
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: 53.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.947 Å20.474 Å20 Å2
2--0.947 Å2-0 Å2
3----3.072 Å2
Refinement stepCycle: LAST / Resolution: 1.8→54.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 31 166 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122959
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162842
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.8323998
X-RAY DIFFRACTIONr_angle_other_deg0.3971.7766569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0525360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.3359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40410544
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.87110135
X-RAY DIFFRACTIONr_chiral_restr0.0520.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
X-RAY DIFFRACTIONr_nbd_refined0.2040.2614
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22533
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21464
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21455
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2167
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0780.28
X-RAY DIFFRACTIONr_nbd_other0.1430.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.212
X-RAY DIFFRACTIONr_mcbond_it2.3744.2471447
X-RAY DIFFRACTIONr_mcbond_other2.3724.2471446
X-RAY DIFFRACTIONr_mcangle_it3.8447.6211804
X-RAY DIFFRACTIONr_mcangle_other3.8447.6251805
X-RAY DIFFRACTIONr_scbond_it2.7334.6351512
X-RAY DIFFRACTIONr_scbond_other2.7334.6361513
X-RAY DIFFRACTIONr_scangle_it4.498.3832194
X-RAY DIFFRACTIONr_scangle_other4.4898.3842195
X-RAY DIFFRACTIONr_lrange_it7.40438.7973344
X-RAY DIFFRACTIONr_lrange_other7.3738.4493304
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
1.8-1.8470.4271570.44133120.44134730.7940.80499.88480.444
1.847-1.8970.4291930.40432120.40634080.8280.83999.9120.403
1.897-1.9520.3631520.3831550.37933150.8440.85999.75870.368
1.952-2.0120.3741790.33130380.33432230.8650.89599.81380.318
2.012-2.0780.331700.30629750.30831490.9140.91899.8730.285
2.078-2.1510.2851650.26728560.26830240.9370.94599.90080.236
2.151-2.2320.2941420.24927940.25129400.9370.95399.86390.214
2.232-2.3230.2641570.23426830.23628450.9560.96299.82430.203
2.323-2.4260.2631540.22725400.2327010.9590.96799.74080.189
2.426-2.5440.2781170.22125190.22326400.9590.9799.84850.183
2.544-2.6820.261020.21323820.21424870.9570.97399.87940.177
2.682-2.8440.3161080.2222610.22423750.950.97299.74740.181
2.844-3.040.2551240.22621180.22822450.9620.9799.86640.195
3.04-3.2820.2371180.22419650.22520960.9660.9799.37980.198
3.282-3.5940.273790.21418360.21619460.9490.97398.4070.197
3.594-4.0160.237900.18516670.18717840.9670.9898.48650.169
4.016-4.6340.179720.16114920.16215810.980.98598.92470.148
4.634-5.6650.207660.1913210.19113900.9770.97999.78420.172
5.665-7.9690.302460.22710500.2310960.9520.9691000.207
7.969-54.9520.153390.2096580.2066970.990.9741000.177
Refinement TLS params.Method: refined / Origin x: 23.2248 Å / Origin y: 55.671 Å / Origin z: 22.0369 Å
111213212223313233
T0.1795 Å20.1074 Å2-0.0067 Å2-0.1384 Å20.027 Å2--0.0224 Å2
L0.3347 °20.0093 °2-0.4262 °2-0.3681 °20.1721 °2--0.9792 °2
S0.0141 Å °0.028 Å °0.029 Å °-0.1101 Å °-0.0572 Å °0.0498 Å °-0.1449 Å °-0.0064 Å °0.0431 Å °
Refinement TLS groupSelection: ALL

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