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Yorodumi- PDB-2jdl: Structure of C-terminal region of acidic P2 ribosomal protein com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jdl | ||||||
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Title | Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin | ||||||
Components |
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Keywords | HYDROLASE / RIBOSOME INACTIVIATING PROTEIN / RIBOSOMAL PROTEIN / PROTEIN SYNTHESIS INHIBITOR / TOXIN / PLANT DEFENSE / ANTIVIRAL PROTEIN | ||||||
Function / homology | Function and homology information cytoplasmic translational elongation / regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane ...cytoplasmic translational elongation / regulation of defense response to virus / rRNA N-glycosylase / rRNA N-glycosylase activity / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / defense response / Regulation of expression of SLITs and ROBOs / cytoplasmic translation / cytosolic large ribosomal subunit / toxin activity / negative regulation of translation / structural constituent of ribosome / translation / focal adhesion / extracellular exosome / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | TRICHOSANTHES KIRILOWII (gua lou) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Too, P.H. / Mak, A.N. / Zhu, G. / Au, S.W. / Wong, K.B. / Shaw, P.C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: The C-Terminal Fragment of the Ribosomal P Protein Complexed to Trichosanthin Reveals the Interaction between the Ribosome-Inactivating Protein and the Ribosome. Authors: Too, P.H. / Ma, M.K. / Mak, A.N. / Wong, Y.T. / Tung, C.K. / Zhu, G. / Au, S.W. / Wong, K.B. / Shaw, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jdl.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jdl.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/2jdl ftp://data.pdbj.org/pub/pdb/validation_reports/jd/2jdl | HTTPS FTP |
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-Related structure data
Related structure data | 2jjrC 2vs6C 1tcsS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 27182.877 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-270 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRICHOSANTHES KIRILOWII (gua lou) / Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P09989, rRNA N-glycosylase #2: Protein/peptide | Mass: 1218.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P05387*PLUS #3: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.6 % / Description: NONE |
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Crystal grow | Details: 7% PEG 20000, 0.1M MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: VARIMAX HR |
Radiation | Monochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→92 Å / Num. obs: 24055 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.2 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TCS Resolution: 2.2→25.47 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.878 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.225 / 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: 19.34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→25.47 Å
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Refine LS restraints |
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