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- PDB-8dcn: Crystal structure of Clostridioides difficile binary toxin CDTb D... -

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Basic information

Entry
Database: PDB / ID: 8dcn
TitleCrystal structure of Clostridioides difficile binary toxin CDTb D4 fragment in complex with BINTOXB/9 Fab
Components
  • ADP-ribosylating binary toxin binding subunit CdtB
  • BINTOXB/9 Fab heavy chain
  • BINTOXB/9 Fab light chain
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 ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.6 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BINTOXB/9 Fab heavy chain
B: BINTOXB/9 Fab light chain
C: ADP-ribosylating binary toxin binding subunit CdtB
D: BINTOXB/9 Fab heavy chain
E: BINTOXB/9 Fab light chain
F: ADP-ribosylating binary toxin binding subunit CdtB


Theoretical massNumber of molelcules
Total (without water)129,0926
Polymers129,0926
Non-polymers00
Water1,42379
1
A: BINTOXB/9 Fab heavy chain
B: BINTOXB/9 Fab light chain
C: ADP-ribosylating binary toxin binding subunit CdtB


Theoretical massNumber of molelcules
Total (without water)64,5463
Polymers64,5463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: BINTOXB/9 Fab heavy chain
E: BINTOXB/9 Fab light chain
F: ADP-ribosylating binary toxin binding subunit CdtB


Theoretical massNumber of molelcules
Total (without water)64,5463
Polymers64,5463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.209, 111.760, 148.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 126 or resid 134 through 213))
d_2ens_1(chain "D" and (resid 1 through 126 or resid 134 through 213))
d_1ens_2chain "B"
d_2ens_2chain "E"
d_1ens_3chain "C"
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNPROPROAA1 - 1261 - 133
d_12ens_1SERSERARGARGAA134 - 213141 - 220
d_21ens_1GLNGLNPROPRODD1 - 1261 - 133
d_22ens_1SERSERARGARGDD134 - 213141 - 220
d_11ens_2ASPASPGLUGLUBB1 - 2121 - 218
d_21ens_2ASPASPGLUGLUEE1 - 2121 - 218
d_11ens_3ILEILEVALVALCC755 - 8753 - 123
d_21ens_3ILEILEVALVALFF755 - 8753 - 123

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

#1: Antibody BINTOXB/9 Fab heavy chain


Mass: 25075.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody BINTOXB/9 Fab light chain


Mass: 24210.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein ADP-ribosylating binary toxin binding subunit CdtB / ADP-ribosyltransferase binding component / CdtB


Mass: 15259.141 Da / Num. of mol.: 2 / Fragment: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10.1% PEG3350, 13.4% 2-propanol, 0.2 M ammonium citrate pH 7.5

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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: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→55.88 Å / Num. obs: 50515 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 58.05 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.2
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 4574 / CC1/2: 0.61

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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: 2.6→55.88 Å / SU ML: 0.3775 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6504
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2603 2482 4.91 %
Rwork0.2265 48033 -
obs0.2281 50515 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.54 Å2
Refinement stepCycle: LAST / Resolution: 2.6→55.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8644 0 0 79 8723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00268854
X-RAY DIFFRACTIONf_angle_d0.581212044
X-RAY DIFFRACTIONf_chiral_restr0.04251337
X-RAY DIFFRACTIONf_plane_restr0.0051531
X-RAY DIFFRACTIONf_dihedral_angle_d14.61593206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.639258449078
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.840453704191
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.639216406855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.32931480.34392628X-RAY DIFFRACTION99.5
2.65-2.70.34021290.3382621X-RAY DIFFRACTION99.49
2.7-2.760.38781760.33612601X-RAY DIFFRACTION99.28
2.76-2.830.36331210.32112647X-RAY DIFFRACTION99.6
2.83-2.90.34291260.30962661X-RAY DIFFRACTION99.39
2.9-2.980.36941310.3312661X-RAY DIFFRACTION99.04
2.98-3.060.38761110.32162643X-RAY DIFFRACTION99.64
3.06-3.160.31451570.29052648X-RAY DIFFRACTION99.36
3.16-3.280.28681300.27492658X-RAY DIFFRACTION99.54
3.28-3.410.31721310.26692646X-RAY DIFFRACTION99.36
3.41-3.560.29181390.25342667X-RAY DIFFRACTION99.12
3.56-3.750.25431390.24522656X-RAY DIFFRACTION99.18
3.75-3.980.28061330.2142676X-RAY DIFFRACTION99.79
3.98-4.290.23551600.19042672X-RAY DIFFRACTION99.26
4.29-4.720.18821370.17142664X-RAY DIFFRACTION98.87
4.72-5.410.20441480.1692723X-RAY DIFFRACTION99.41
5.41-6.810.23671340.19492745X-RAY DIFFRACTION99.41
6.81-55.880.20681320.17392816X-RAY DIFFRACTION96.85

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