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Yorodumi- PDB-7ubx: Structure of a pore forming fragment of Clostridium difficile tox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ubx | ||||||
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Title | Structure of a pore forming fragment of Clostridium difficile toxin A in complex with VHH AA6 | ||||||
Components |
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Keywords | TOXIN / pore forming / neutralizing antibody | ||||||
Function / homology | Function and homology information 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 | Clostridioides difficile (bacteria) Camelidae (mammal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Chen, B. / Rongsheng, J. / Kay, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Front Immunol / Year: 2022 Title: Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies. Authors: Chen, B. / Perry, K. / Jin, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ubx.cif.gz | 250.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ubx.ent.gz | 158.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ubx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ubx_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 7ubx_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 7ubx_validation.xml.gz | 35 KB | Display | |
Data in CIF | 7ubx_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/7ubx ftp://data.pdbj.org/pub/pdb/validation_reports/ub/7ubx | HTTPS FTP |
-Related structure data
Related structure data | 7ubyC 5m2jS 7u1zS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 43746.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdA, toxA / Production host: Escherichia coli (E. coli) References: UniProt: P16154, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Antibody | Mass: 12995.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium acetate, 0.1 M Bis-Tris, pH 5.7, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→54.65 Å / Num. obs: 88827 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 31.11 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.85 |
Reflection shell | Resolution: 1.81→1.88 Å / Num. unique obs: 8321 / CC1/2: 0.702 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7U1Z, 5M2J Resolution: 1.81→54.65 Å / SU ML: 0.2493 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.9725 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→54.65 Å
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Refine LS restraints |
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LS refinement shell |
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