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- PDB-5uqn: Clostridium difficile Toxin B (TcdB) glucosyltransferase domain i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uqn | ||||||||||||
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Title | Clostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F | ||||||||||||
![]() | Toxin B | ||||||||||||
![]() | TRANSFERASE / Glucosyltransferase / Toxin / HYDROLASE | ||||||||||||
Function / homology | ![]() glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 | ![]() ![]() ![]() | ||||||||||||
![]() | Alvin, J.W. / Lacy, D.B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Clostridium difficile toxin glucosyltransferase domains in complex with a non-hydrolyzable UDP-glucose analogue. Authors: Alvin, J.W. / Lacy, D.B. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 340.6 KB | Display | ![]() |
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PDB format | ![]() | 280.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 846.5 KB | Display | ![]() |
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Full document | ![]() | 852.2 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uqkC ![]() 5uqlC ![]() 5uqmC ![]() 5uqtC ![]() 2bvlS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 65356.988 Da / Num. of mol.: 1 / Fragment: residues 1-543 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases | ||
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#2: Chemical | ChemComp-MN / | ||
#3: Chemical | ChemComp-U2F / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % / Description: Short bars. |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 0.2 M ammonium sulfate, PEG 8k 16-34% / PH range: 6-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→54.67 Å / Num. obs: 41228 / % possible obs: 99.1 % / Redundancy: 11.2 % / CC1/2: 0.946 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2BVL Resolution: 2.06→54.19 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→54.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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