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- PDB-8dcm: Crystal structure of Clostridioides difficile binary toxin proCDT... -

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Basic information

Entry
Database: PDB / ID: 8dcm
TitleCrystal structure of Clostridioides difficile binary toxin proCDTb lacking D4 in complex with BINTOXB/22 Fab
Components
  • (BINTOXB/22 Fab ...) x 2
  • ADP-ribosylating binary toxin binding subunit CdtB
KeywordsTOXIN/IMMUNE SYSTEM / virulence / antibodies / neutralization / bacteria / TOXIN / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


protein homooligomerization / transferase activity / extracellular region / metal ion binding / identical protein binding
Similarity search - Function
Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 domain / PA14 / PA14 domain
Similarity search - Domain/homology
ADP-ribosyltransferase binding component
Similarity search - Component
Biological speciesMus musculus (house mouse)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGoldsmith, J.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: J.Bacteriol. / Year: 2023
Title: Structural Basis for Binding of Neutralizing Antibodies to Clostridioides difficile Binary Toxin.
Authors: Goldsmith, J.A. / Dewar, V. / Hermand, P. / Blais, N. / McLellan, J.S.
History
DepositionJun 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BINTOXB/22 Fab heavy chain
B: BINTOXB/22 Fab light chain
C: ADP-ribosylating binary toxin binding subunit CdtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,4897
Polymers128,3463
Non-polymers1434
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.229, 118.480, 166.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules C

#3: Protein ADP-ribosylating binary toxin binding subunit CdtB / ADP-ribosyltransferase binding component / CdtB / proCDTb


Mass: 80041.344 Da / Num. of mol.: 1 / Fragment: lacking D4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtB, E5F34_11700 / Production host: Escherichia coli (E. coli) / References: UniProt: A8DS70

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Antibody , 2 types, 2 molecules AB

#1: Antibody BINTOXB/22 Fab heavy chain


Mass: 24862.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody BINTOXB/22 Fab light chain


Mass: 23441.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 263 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG8000, 0.09 M sodium nitrate, 0.09 M sodium phosphate dibasic, 0.09 M ammonium sulfate, 0.1 M imidazole pH 6.5, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→96.46 Å / Num. obs: 45722 / % possible obs: 93.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 28.11 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.5
Reflection shellResolution: 2.5→2.58 Å / Num. unique obs: 3686 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.19.2refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UWT

6uwt


Resolution: 2.5→59.24 Å / SU ML: 0.2382 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 2204 4.82 %
Rwork0.1976 43518 -
obs0.199 45722 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→59.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8813 0 4 259 9076
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00298997
X-RAY DIFFRACTIONf_angle_d0.642512215
X-RAY DIFFRACTIONf_chiral_restr0.04371364
X-RAY DIFFRACTIONf_plane_restr0.00391580
X-RAY DIFFRACTIONf_dihedral_angle_d15.43623311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.30371140.2622397X-RAY DIFFRACTION83.28
2.55-2.610.30411290.25352372X-RAY DIFFRACTION83.95
2.61-2.680.25191290.23942486X-RAY DIFFRACTION87.34
2.68-2.750.29561450.24422556X-RAY DIFFRACTION89.5
2.75-2.830.31751110.24222438X-RAY DIFFRACTION84.49
2.83-2.920.26781430.23932756X-RAY DIFFRACTION95.8
2.92-3.030.24241400.23762822X-RAY DIFFRACTION98.8
3.03-3.150.27821170.21712835X-RAY DIFFRACTION98.14
3.15-3.290.25021590.2152854X-RAY DIFFRACTION98.85
3.29-3.470.21891480.21372863X-RAY DIFFRACTION99.37
3.47-3.680.2291200.1832725X-RAY DIFFRACTION93.62
3.68-3.970.20911620.17692795X-RAY DIFFRACTION97.01
3.97-4.370.17771480.16432917X-RAY DIFFRACTION99.61
4.37-50.19751430.15072928X-RAY DIFFRACTION99.61
5-6.30.21161530.18352769X-RAY DIFFRACTION93.83
6.3-59.240.1721430.17623005X-RAY DIFFRACTION96.09

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