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- PDB-7uby: Structure of the GTD domain of Clostridium difficile toxin A in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7uby | ||||||
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Title | Structure of the GTD domain of Clostridium difficile toxin A in complex with VHH AH3 | ||||||
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![]() | TOXIN / GTD / neutralizing antibody | ||||||
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 / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, B. / Rongsheng, J. / Kay, P. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 302.7 KB | Display | ![]() |
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PDB format | ![]() | 218.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 50.2 KB | Display | |
Data in CIF | ![]() | 70.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ubxC ![]() 6oq5S S: Starting model for refinement 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Antibody , 2 types, 4 molecules BADC
#1: Protein | Mass: 62918.996 Da / Num. of mol.: 2 / Mutation: K190A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P16154, Transferases; Glycosyltransferases; Hexosyltransferases #2: Antibody | Mass: 16113.987 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 358 molecules ![](data/chem/img/UPG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium phosphate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 28, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→78.73 Å / Num. obs: 94481 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 33.23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Net I/σ(I): 12.5 / Num. measured all: 328473 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OQ5 Resolution: 2.1→67.57 Å / SU ML: 0.2988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2895 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→67.57 Å
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Refine LS restraints |
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LS refinement shell |
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