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Basic information

Entry
Database: PDB / ID: 7so7
TitleNovel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B
Components
  • FAB B1 LC
  • Fab B1 HC
  • Toxin B
KeywordsTOXIN/IMMUNE SYSTEM / antibody / toxin / TcdB / epitope / Clostridium difficile toxin / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane ...symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / membrane
Similarity search - Function
TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain ...TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridioides difficile (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsLiu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B.
Authors: Liu, J. / Kothe, M. / Zhang, J. / Oloo, E. / Stegalkina, S. / Mundle, S.T. / Li, L. / Zhang, J. / Cole, L.E. / Barone, L. / Biemann, H.P. / Kleanthous, H. / Anosova, N.G. / Anderson, S.F.
History
DepositionOct 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin B
B: Toxin B
X: Fab B1 HC
Y: FAB B1 LC
H: Fab B1 HC
L: FAB B1 LC


Theoretical massNumber of molelcules
Total (without water)217,5386
Polymers217,5386
Non-polymers00
Water00
1
A: Toxin B
H: Fab B1 HC
L: FAB B1 LC


Theoretical massNumber of molelcules
Total (without water)108,7693
Polymers108,7693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toxin B
X: Fab B1 HC
Y: FAB B1 LC


Theoretical massNumber of molelcules
Total (without water)108,7693
Polymers108,7693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)210.540, 320.080, 65.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Toxin B


Mass: 62652.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Production host: Escherichia coli (E. coli)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Antibody Fab B1 HC


Mass: 22804.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody FAB B1 LC


Mass: 23312.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
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: 5.14 Å3/Da / Density % sol: 76.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na cacodylate, 0.2M CaCl2, 40% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.59→74.8 Å / Num. obs: 53178 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 91.16 Å2 / Rpim(I) all: 0.107 / Net I/σ(I): 8.6
Reflection shellResolution: 3.59→3.68 Å / Num. unique obs: 3907 / Rpim(I) all: 0.557 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D69

3d69


Resolution: 3.59→74.8 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2583 1998 3.76 %
Rwork0.2094 51077 -
obs0.2113 53075 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 229.94 Å2 / Biso mean: 93.2865 Å2 / Biso min: 48.31 Å2
Refinement stepCycle: final / Resolution: 3.59→74.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15130 0 0 0 15130
Num. residues----1919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415450
X-RAY DIFFRACTIONf_angle_d0.70220936
X-RAY DIFFRACTIONf_chiral_restr0.0432322
X-RAY DIFFRACTIONf_plane_restr0.0062692
X-RAY DIFFRACTIONf_dihedral_angle_d7.0269296
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5901-3.67990.33941420.31433628100
3.6799-3.77940.35841390.29523535100
3.7794-3.89060.30031420.27023641100
3.8906-4.01610.37461390.27333545100
4.0161-4.15970.28251410.23483605100
4.1597-4.32620.25131420.20663609100
4.3262-4.52310.25031390.18893591100
4.5231-4.76150.23871430.18223640100
4.7615-5.05970.21561430.17843656100
5.0597-5.45030.2511420.18193642100
5.4503-5.99860.24751430.20593671100
5.9986-6.86610.27551440.2153666100
6.8661-8.64850.20111460.18593727100
8.6485-74.80.23241530.1805392199
Refinement TLS params.Method: refined / Origin x: -48.8271 Å / Origin y: 80.1 Å / Origin z: -24.0886 Å
111213212223313233
T0.6109 Å20.0534 Å2-0.0014 Å2-0.6277 Å20.0131 Å2--0.5751 Å2
L0.1912 °20.2789 °2-0.0535 °2-0.2524 °2-0.01 °2--0.2696 °2
S-0.0503 Å °0.0581 Å °-0.0082 Å °0.1111 Å °0.0837 Å °-0.0005 Å °-0.0215 Å °-0.0076 Å °-0.0329 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 535
2X-RAY DIFFRACTION1allB1 - 538
3X-RAY DIFFRACTION1allX1 - 219
4X-RAY DIFFRACTION1allY1 - 218
5X-RAY DIFFRACTION1allH1 - 219
6X-RAY DIFFRACTION1allL1 - 218

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