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- PDB-7ubx: Structure of a pore forming fragment of Clostridium difficile tox... -

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Basic information

Entry
Database: PDB / ID: 7ubx
TitleStructure of a pore forming fragment of Clostridium difficile toxin A in complex with VHH AA6
Components
  • Nanobody VHH AA6
  • Toxin A
KeywordsTOXIN / pore forming / neutralizing antibody
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / glycosyltransferase activity / 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 ...Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / glycosyltransferase activity / 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)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsChen, B. / Rongsheng, J. / Kay, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Immunol / Year: 2022
Title: Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies.
Authors: Chen, B. / Perry, K. / Jin, R.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 25, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Toxin A
D: Nanobody VHH AA6
B: Toxin A
C: Nanobody VHH AA6


Theoretical massNumber of molelcules
Total (without water)113,4844
Polymers113,4844
Non-polymers00
Water3,027168
1
A: Toxin A
D: Nanobody VHH AA6


Theoretical massNumber of molelcules
Total (without water)56,7422
Polymers56,7422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-3 kcal/mol
Surface area20630 Å2
MethodPISA
2
B: Toxin A
C: Nanobody VHH AA6


Theoretical massNumber of molelcules
Total (without water)56,7422
Polymers56,7422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.018, 85.995, 109.339
Angle α, β, γ (deg.)90.000, 91.452, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Toxin A


Mass: 43746.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdA, toxA / Production host: Escherichia coli (E. coli)
References: UniProt: P16154, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Antibody Nanobody VHH AA6


Mass: 12995.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Bis-Tris, pH 5.7, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.81→54.65 Å / Num. obs: 88827 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.85
Reflection shellResolution: 1.81→1.88 Å / Num. unique obs: 8321 / CC1/2: 0.702

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U1Z, 5M2J

7u1z

5m2j


Resolution: 1.81→54.65 Å / SU ML: 0.2493 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2456 2015 2.27 %
Rwork0.2134 86812 -
obs0.2141 88827 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.31 Å2
Refinement stepCycle: LAST / Resolution: 1.81→54.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7664 0 0 168 7832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717807
X-RAY DIFFRACTIONf_angle_d0.938810616
X-RAY DIFFRACTIONf_chiral_restr0.06271252
X-RAY DIFFRACTIONf_plane_restr0.00811350
X-RAY DIFFRACTIONf_dihedral_angle_d6.18031076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.860.31421360.33075655X-RAY DIFFRACTION89.59
1.86-1.910.34081450.29346168X-RAY DIFFRACTION98.5
1.91-1.960.33251310.26556198X-RAY DIFFRACTION98.77
1.96-2.030.2721510.25146244X-RAY DIFFRACTION98.7
2.03-2.10.29121410.24486200X-RAY DIFFRACTION98.45
2.1-2.180.30061390.24426121X-RAY DIFFRACTION96.86
2.18-2.280.32481510.24266297X-RAY DIFFRACTION99.78
2.28-2.40.291460.23696278X-RAY DIFFRACTION99.78
2.4-2.560.31841470.24016324X-RAY DIFFRACTION99.54
2.56-2.750.27151470.24766230X-RAY DIFFRACTION98.87
2.75-3.030.29641400.24536246X-RAY DIFFRACTION98.38
3.03-3.470.24241430.22146261X-RAY DIFFRACTION98.54
3.47-4.370.20241430.17866242X-RAY DIFFRACTION98.05
4.37-54.650.17841550.16316348X-RAY DIFFRACTION98.25

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