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Yorodumi- PDB-5y48: Crystal structure of the complex of Ribosome inactivating protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y48 | ||||||
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Title | Crystal structure of the complex of Ribosome inactivating protein from Momordica balsamina with Pyrimidine-2,4-dione at 1.70 Angstrom resolution | ||||||
Components | Ribosome inactivating proteinRibosome-inactivating protein | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / nucleotide binding Similarity search - Function | ||||||
Biological species | Momordica balsamina (balsam apple) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Singh, P.K. / Pandey, S. / Iqbal, N. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: Proteins / Year: 2019 Title: Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with uracil and uridine. Authors: Pandey, S.N. / Iqbal, N. / Singh, P.K. / Rastogi, N. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y48.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y48.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 5y48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/5y48 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/5y48 | HTTPS FTP |
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-Related structure data
Related structure data | 5ilwC 5ilxS S: Starting model for refinement C: citing same article (ref.) |
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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: 27093.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica balsamina (balsam apple) / References: UniProt: D9J2T9, rRNA N-glycosylase |
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#2: Chemical | ChemComp-URA / |
#3: Sugar | ChemComp-NAG / |
#4: 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: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 14% PEG 6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 22, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→65.09 Å / Num. obs: 27751 / % possible obs: 100 % / Redundancy: 2 % / Rsym value: 0.04 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.701→1.745 Å / Mean I/σ(I) obs: 2.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ILX Resolution: 1.7→65.09 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.25 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.218 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→65.09 Å
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Refine LS restraints |
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