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- PDB-8bgm: Crystal structure of the OrfX1-OrfX3 complex from the PMP1 neurot... -

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Basic information

Entry
Database: PDB / ID: 8bgm
TitleCrystal structure of the OrfX1-OrfX3 complex from the PMP1 neurotoxin gene cluster
Components(Toxin) x 2
KeywordsTOXIN / PMP1 Clostridial neurotoxins OrfX gene cluster Botulinum TULIP
Function / homologyClostridium P47 protein / Clostridium P-47-like / toxin activity / Protein OrfX3 / Protein OrfX1
Function and homology information
Biological speciesParaclostridium bifermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKosenina, S. / Stenmark, P.
Funding support Denmark, Sweden, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20OC0064789 Denmark
Swedish Research Council2018-03406 Sweden
CitationJournal: Febs Lett. / Year: 2023
Title: Crystal structure of the OrfX1-OrfX3 complex from the PMP1 neurotoxin gene cluster.
Authors: Kosenina, S. / Stenmark, P.
History
DepositionOct 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 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
A: Toxin
B: Toxin
C: Toxin
D: Toxin


Theoretical massNumber of molelcules
Total (without water)147,1974
Polymers147,1974
Non-polymers00
Water00
1
A: Toxin
B: Toxin


Theoretical massNumber of molelcules
Total (without water)73,5992
Polymers73,5992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-15 kcal/mol
Surface area26700 Å2
MethodPISA
2
C: Toxin
D: Toxin


Theoretical massNumber of molelcules
Total (without water)73,5992
Polymers73,5992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-16 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.018, 126.573, 154.218
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 Toxin / OrfX1


Mass: 18546.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: OrfX1
Source: (gene. exp.) Paraclostridium bifermentans (bacteria)
Gene: D4A35_18135 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5P3XKM0
#2: Protein Toxin / OrfX3


Mass: 55052.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: OrfX3
Source: (gene. exp.) Paraclostridium bifermentans (bacteria)
Gene: D4A35_18125 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5P3XKL3

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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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.7→77.1 Å / Num. obs: 50841 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.99 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.06 / Rrim(I) all: 0.16 / Net I/σ(I): 8.5
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.56 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4574 / CC1/2: 0.742 / % possible all: 99.1

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Processing

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

Resolution: 2.7→63.367 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.219 / Average fsc free: 0.7891 / Average fsc work: 0.7991 / Cross valid method: FREE R-VALUE / ESU R: 0.622 / ESU R Free: 0.324 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2629 2545 5.02 %
Rwork0.2224 48156 -
all0.224 --
obs-50701 99.917 %
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: 53.008 Å2
Baniso -1Baniso -2Baniso -3
1-12.337 Å2-0 Å20 Å2
2---4.639 Å20 Å2
3----7.698 Å2
Refinement stepCycle: LAST / Resolution: 2.7→63.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9696 0 0 0 9696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0129894
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.62313380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57651202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.00224.509499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.307151767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8411531
X-RAY DIFFRACTIONr_chiral_restr0.1030.21284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027415
X-RAY DIFFRACTIONr_nbd_refined0.2160.23961
X-RAY DIFFRACTIONr_nbtor_refined0.3120.26823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2190
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.24
X-RAY DIFFRACTIONr_mcbond_it2.425.0844838
X-RAY DIFFRACTIONr_mcangle_it3.9167.6216030
X-RAY DIFFRACTIONr_scbond_it2.8785.4315056
X-RAY DIFFRACTIONr_scangle_it4.7738.0027350
X-RAY DIFFRACTIONr_lrange_it6.8967.89114204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.4461680.4343529X-RAY DIFFRACTION99.8649
2.928-3.0180.3691850.33245X-RAY DIFFRACTION99.9417

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