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Yorodumi- PDB-8i7p: Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i7p | ||||||
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Title | Crystal structure of Ricin A chain bound with N2-(2-amino-4-oxo-3,4-dihydropteridine-7-carbonyl)glycyl-L-tyrosine | ||||||
Components |
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Keywords | HYDROLASE / Toxin / Inhibitor | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Goto, M. / Sakamoto, N. / Higashi, S. / Kawata, R. / Nagatsu, K. / Saito, R. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J Enzyme Inhib Med Chem / Year: 2023 Title: Crystal structure of ricin toxin A chain complexed with a highly potent pterin-based small-molecular inhibitor. Authors: Goto, M. / Sakamoto, N. / Higashi, S. / Kawata, R. / Nagatsu, K. / Saito, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i7p.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i7p.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 8i7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/8i7p ftp://data.pdbj.org/pub/pdb/validation_reports/i7/8i7p | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30896.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02879, rRNA N-glycosylase | ||||
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#2: Protein/peptide | Mass: 427.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG2000, Lithium sulfate, Sodium acetate |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→48.93 Å / Num. obs: 43942 / % possible obs: 99.2 % / Redundancy: 13 % / CC1/2: 1 / Rpim(I) all: 0.012 / Rrim(I) all: 0.042 / Net I/σ(I): 35.6 / Num. measured all: 571567 |
Reflection shell | Resolution: 1.6→1.69 Å / % possible obs: 98.3 % / Redundancy: 13.6 % / Num. measured all: 84549 / Num. unique obs: 6237 / CC1/2: 0.912 / Rpim(I) all: 0.214 / Rrim(I) all: 0.801 / Net I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.72 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.09 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.051 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→48.93 Å
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