+Open data
-Basic information
Entry | Database: PDB / ID: 4nby | ||||||
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Title | Crystal Structure of TcdA-A2 Bound to Two Molecules of A20.1 VHH | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody-antigen complex | ||||||
Function / homology | Cholin Binding / left handed beta-beta-3-solenoid / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Clostridium difficile (bacteria) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Murase, T. / Eugenio, L. / Schorr, M. / Hussack, G. / Tanha, J. / Kitova, E. / Klassen, J.S. / Ng, K.K.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nby.cif.gz | 118.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nby.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 4nby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/4nby ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nby | HTTPS FTP |
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-Related structure data
Related structure data | 4nbxC 4nbzC 4nc0C 4nc1C 4nc2C 2g7cS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29547.760 Da / Num. of mol.: 1 / Fragment: UNP residues 1-248 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 48489 / Gene: HMPREF0219_0762, TcdA / Production host: Escherichia coli (E. coli) / References: UniProt: D5RWT1 | ||
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#2: Antibody | Mass: 16828.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Gene: VHH / Production host: Escherichia coli (E. coli) #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.1 M Ammonium sulfate, 0.1 M Tris-Cl, pH 7.5, 0.1 M TMAO, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2012 / Details: mirrors |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→40 Å / Num. all: 48737 / Num. obs: 48737 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.08→2.13 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3513 / Rsym value: 0.692 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2G7C Resolution: 2.08→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.121 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 34.296 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.134 Å / Total num. of bins used: 20
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