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Yorodumi- PDB-3n2d: Crystal Structure of the Complex of type I Ribosome inactivating ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n2d | |||||||||
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Title | Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution | |||||||||
Components |
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Keywords | HYDROLASE / RIP / Hexapeptide / Plant protein | |||||||||
Function / homology | Function and homology information cytoplasmic translational elongation / fungal-type vacuole / rRNA N-glycosylase / rRNA N-glycosylase activity / molecular function inhibitor activity / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...cytoplasmic translational elongation / fungal-type vacuole / rRNA N-glycosylase / rRNA N-glycosylase activity / molecular function inhibitor activity / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / toxin activity / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / structural constituent of ribosome / nucleotide binding / cytosol Similarity search - Function | |||||||||
Biological species | Momordica balsamina (balsam apple) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | |||||||||
Authors | Kushwaha, G.S. / Prem Kumar, R. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: To be Published Title: Crystal Structure of the Complex of type I Ribosome inactivating protein with hexapeptide Ser-Asp-Asp-Asp-Met-Gly at 2.2 A resolution Authors: Kushwaha, G.S. / Prem Kumar, R. / Sinha, M. / Bhushan, A. / 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 | 3n2d.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n2d.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 3n2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n2d_validation.pdf.gz | 907.8 KB | Display | wwPDB validaton report |
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Full document | 3n2d_full_validation.pdf.gz | 911.3 KB | Display | |
Data in XML | 3n2d_validation.xml.gz | 14 KB | Display | |
Data in CIF | 3n2d_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/3n2d ftp://data.pdbj.org/pub/pdb/validation_reports/n2/3n2d | HTTPS FTP |
-Related structure data
Related structure data | 1ahaS S: Starting model for refinement |
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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*PLUS, rRNA N-glycosylase |
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#2: Protein/peptide | Mass: 638.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02400 |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE HAS BEEN DEPOSITED ON GENBANK WITH ACCESSION CODE, HM367595. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 % |
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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: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5414 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2009 / Details: Mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5414 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→65.7 Å / Num. all: 12968 / Num. obs: 12968 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 42.124 Å2 / Rsym value: 0.056 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.22→2.29 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.315 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AHA Resolution: 2.22→19.84 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.207 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.238 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.229 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.217→2.275 Å / Total num. of bins used: 20
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