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Yorodumi- PDB-4kuc: Crystal structure of ricin-A chain in complex with the antibody 6C2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kuc | ||||||
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Title | Crystal structure of ricin-A chain in complex with the antibody 6C2 | ||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / RNA-N-glycosidase / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation Similarity search - Function | ||||||
Biological species | Ricinus communis (castor bean) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.787 Å | ||||||
Authors | Zhu, Y. / Li, X. / Teng, M. | ||||||
Citation | Journal: To be Published Title: Structural insights into the neutralization mechanism of mAb 6C2 against ricin Authors: Zhu, Y. / Li, X. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kuc.cif.gz | 216.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kuc.ent.gz | 176.2 KB | Display | PDB format |
PDBx/mmJSON format | 4kuc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/4kuc ftp://data.pdbj.org/pub/pdb/validation_reports/ku/4kuc | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 29936.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase #2: Antibody | Mass: 25401.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybridoma #3: Antibody | Mass: 25257.236 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: Hybridoma |
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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: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M Nacitrate,ph 5.0, 8% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 0.9792 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.787→50 Å / Num. obs: 40594 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.787→36.436 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 34.17 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.787→36.436 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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