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- PDB-5uql: Clostridium difficile toxin A (TcdA) glucosyltransferase domain i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uql | ||||||||||||
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Title | Clostridium difficile toxin A (TcdA) glucosyltransferase domain in complex with U2F | ||||||||||||
![]() | Toxin A | ||||||||||||
![]() | TRANSFERASE / glucosyltransferase / toxin | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | 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 | ![]() | 236.9 KB | Display | ![]() |
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PDB format | ![]() | 190.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5uqkC ![]() 5uqmC ![]() 5uqnC ![]() 5uqtC ![]() 3srzS 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: 64712.988 Da / Num. of mol.: 1 / Fragment: residues 1-544 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P16154, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-U2F / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.86 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 0.2 M L-proline PEG 3350, 10-25% / PH range: 7-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→46.518 Å / Num. obs: 51462 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.576 / Net I/σ(I): 21.35 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SRZ Resolution: 1.97→46.518 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.43 / 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: 1.97→46.518 Å
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Refine LS restraints |
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LS refinement shell |
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