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Yorodumi- PDB-7so7: Novel structural insights for a pair of monoclonal antibodies rec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7so7 | ||||||
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Title | Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B | ||||||
Components |
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Keywords | TOXIN/IMMUNE SYSTEM / antibody / toxin / TcdB / epitope / Clostridium difficile toxin / TOXIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å | ||||||
Authors | Liu, J. | ||||||
Funding support | 1items
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Citation | Journal: Curr Res Struct Biol / Year: 2022 Title: Novel structural insights for a pair of monoclonal antibodies recognizing non-overlapping epitopes of the glucosyltransferase domain of Clostridium difficile toxin B. Authors: Liu, J. / Kothe, M. / Zhang, J. / Oloo, E. / Stegalkina, S. / Mundle, S.T. / Li, L. / Zhang, J. / Cole, L.E. / Barone, L. / Biemann, H.P. / Kleanthous, H. / Anosova, N.G. / Anderson, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7so7.cif.gz | 753.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7so7.ent.gz | 632.5 KB | Display | PDB format |
PDBx/mmJSON format | 7so7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/7so7 ftp://data.pdbj.org/pub/pdb/validation_reports/so/7so7 | HTTPS FTP |
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-Related structure data
Related structure data | 7so5C 3d69S C: citing same article (ref.) S: Starting model for refinement |
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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: 62652.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Production host: Escherichia coli (E. coli) References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Antibody | Mass: 22804.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 23312.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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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: 5.14 Å3/Da / Density % sol: 76.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na cacodylate, 0.2M CaCl2, 40% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 3.59→74.8 Å / Num. obs: 53178 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 91.16 Å2 / Rpim(I) all: 0.107 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.59→3.68 Å / Num. unique obs: 3907 / Rpim(I) all: 0.557 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D69 Resolution: 3.59→74.8 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.59 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 229.94 Å2 / Biso mean: 93.2865 Å2 / Biso min: 48.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.59→74.8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -48.8271 Å / Origin y: 80.1 Å / Origin z: -24.0886 Å
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Refinement TLS group |
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