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Open data
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Basic information
Entry | Database: PDB / ID: 4nbz | ||||||
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Title | Crystal Structure of TcdA-A1 Bound to A26.8 VHH | ||||||
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![]() | IMMUNE SYSTEM / Antibody-antigen 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 / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murase, T. / Eugenio, L. / Schorr, M. / Hussack, G. / Tanha, J. / Kitova, E.N. / Klassen, J.S. / Ng, K.K.S. | ||||||
![]() | ![]() Title: Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile. Authors: Murase, T. / Eugenio, L. / Schorr, M. / Hussack, G. / Tanha, J. / Kitova, E.N. / Klassen, J.S. / Ng, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.3 KB | Display | ![]() |
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PDB format | ![]() | 97.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nbxC ![]() 4nbyC ![]() 4nc0C ![]() 4nc1C ![]() 4nc2C ![]() 2f6eS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16288.184 Da / Num. of mol.: 2 / Fragment: UNP residues 2573-2709 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 17010.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 1.5 M Lithium chloride, 12% (w/v) PEG 6000, 0.1 M Citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2010 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 53882 / Num. obs: 53882 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.569 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3513 / Rsym value: 0.56 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2F6E Resolution: 1.75→33.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.905 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.838 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→33.86 Å
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Refine LS restraints |
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