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Yorodumi- PDB-5cst: Structure of the complex of type 1 ribosome inactivating protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cst | |||||||||
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Title | Structure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a nucleotide, cytidine diphosphate at 1.78 A 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: 1.78 Å | |||||||||
Authors | Yamin, S. / Pandey, S. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: Biochem Biophys Rep / Year: 2015 Title: Binding and structural studies of the complexes of type 1 ribosome inactivating protein fromMomordica balsaminawith cytosine, cytidine, and cytidine diphosphate. Authors: Yamini, S. / Pandey, S.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 | 5cst.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cst.ent.gz | 49.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/5cst ftp://data.pdbj.org/pub/pdb/validation_reports/cs/5cst | HTTPS FTP |
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-Related structure data
Related structure data | 4zt8C 4zu0C 4zz6C 5csoC 3s9qS 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: Sugar | ChemComp-NAG / | ||||
#3: Chemical | #4: Chemical | ChemComp-CDP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % |
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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 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 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: 1.78→38.11 Å / Num. all: 22958 / Num. obs: 22958 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rsym value: 0.065 / Net I/σ(I): 34 |
Reflection shell | Resolution: 1.78→1.81 Å / Mean I/σ(I) obs: 2.6 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S9Q Resolution: 1.78→38.11 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.429 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.159 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→38.11 Å
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Refine LS restraints |
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