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- PDB-8yvj: Crystal structure of the C. difficile toxin A CROPs domain fragme... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8yvj | ||||||
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Title | Crystal structure of the C. difficile toxin A CROPs domain fragment 2592-2710 bound to H5.2 nanobody | ||||||
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![]() | TOXIN/IMMUNE SYSTEM / CROPs domain fragment / Toxin A / Complex with nanobody / Clostridioides difficile / TOXIN / TOXIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sluchanko, N.N. / Varfolomeeva, L.A. / Shcheblyakov, D.V. / Belyi, Y.F. / Logunov, D.Y. / Gintsburg, A.L. / Popov, V.O. / Boyko, K.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural insight into recognition of Clostridioides difficile toxin A by novel neutralizing nanobodies targeting QTIN-like motifs within its receptor-binding domain. Authors: Sluchanko, N.N. / Sokolova, I.V. / Favorskaya, I.A. / Esmagambetov, I.B. / Tukhvatulin, A.I. / Alekseeva, I.A. / Ungur, A.S. / Varfolomeeva, L.A. / Boyko, K.M. / Logunov, D.Y. / Gintsburg, A. ...Authors: Sluchanko, N.N. / Sokolova, I.V. / Favorskaya, I.A. / Esmagambetov, I.B. / Tukhvatulin, A.I. / Alekseeva, I.A. / Ungur, A.S. / Varfolomeeva, L.A. / Boyko, K.M. / Logunov, D.Y. / Gintsburg, A.L. / Popov, V.O. / Shcheblyakov, D.V. / Belyi, Y.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.4 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 17.5 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8yvoC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 13645.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13401.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI10463 / Gene: tcdA, toxA / Production host: ![]() ![]() References: UniProt: P16154, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.24 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium phosphate dibasic, pH 8.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 17, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→21.35 Å / Num. obs: 26488 / % possible obs: 98.5 % / Redundancy: 11.1 % / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.009 / Rrim(I) all: 0.032 / Χ2: 0.92 / Net I/σ(I): 54.1 / Num. measured all: 294560 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible obs: 82.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.107 / Num. measured all: 5072 / Num. unique obs: 1095 / CC1/2: 0.983 / Rpim(I) all: 0.055 / Rrim(I) all: 0.121 / Χ2: 0.98 / Net I/σ(I) obs: 12.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.363 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→21.35 Å
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Refine LS restraints |
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