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Open data
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Basic information
Entry | Database: PDB / ID: 4nc1 | ||||||
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Title | Crystal Structure of TcdA-A2 Bound to A20.1 VHH and A26.8 VHH | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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 | ![]() | 197.6 KB | Display | ![]() |
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PDB format | ![]() | 157.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nbxC ![]() 4nbyC ![]() 4nbzC ![]() 4nc0C ![]() 4nc2C ![]() 2g7cS 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: 29547.760 Da / Num. of mol.: 2 / Fragment: UNP residues 1-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Antibody | Mass: 16828.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Antibody | Mass: 14593.076 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 20% (w/v) PEG 4000, 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: RAYONIX MX300HE / Detector: CCD / Date: Sep 5, 2012 / Details: mirrors |
Radiation | Monochromator: Si(111), double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.61→40 Å / Num. all: 47857 / Num. obs: 47857 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.61→2.68 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2284 / Rsym value: 0.719 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2G7C Resolution: 2.61→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.456 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.379 / ESU R Free: 0.274 / 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: 60.044 Å2
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Refinement step | Cycle: LAST / Resolution: 2.61→40 Å
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Refine LS restraints |
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