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Yorodumi- PDB-1vqo: The structure of CCPMN bound to the large ribosomal subunit haloa... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 1vqo | ||||||
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| Title | The structure of CCPMN bound to the large ribosomal subunit haloarcula marismortui | ||||||
Components |
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Keywords | RIBOSOME / ribosome 50S / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX / PROTEIN-RNA COMPLEX / PEPTIDYL TRANSFERASE REACTION | ||||||
| Function / homology | Function and homology informationribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation ...ribonuclease P activity / tRNA 5'-leader removal / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
| Biological species | Haloarcula marismortui (Halophile) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Schmeing, T.M. / Steitz, T.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2005Title: Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction. Authors: Schmeing, T.M. / Huang, K.S. / Kitchen, D.E. / Strobel, S.A. / Steitz, T.A. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 1vqo.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb1vqo.ent.gz | 1.9 MB | Display | PDB format |
| PDBx/mmJSON format | 1vqo.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 1vqo_validation.pdf.gz | 800 KB | Display | wwPDB validaton report |
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| Full document | 1vqo_full_validation.pdf.gz | 1 MB | Display | |
| Data in XML | 1vqo_validation.xml.gz | 315.1 KB | Display | |
| Data in CIF | 1vqo_validation.cif.gz | 497.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/1vqo ftp://data.pdbj.org/pub/pdb/validation_reports/vq/1vqo | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 1vq4C ![]() 1vq5C ![]() 1vq8C ![]() 1vq9C ![]() 1vqkC ![]() 1vqlC ![]() 1vqmC ![]() 1vqpC ![]() 1s72S S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
-RNA chain , 3 types, 3 molecules 094
| #1: RNA chain | Mass: 946090.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
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| #2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
| #3: RNA chain | Mass: 1098.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CYTIDINE-CYTIDINE-PUROMYCIN OLIGOMER |
+50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules ABCDEFHJKLMNOPQRSTUVWXYZ123I
-Protein , 1 types, 1 molecules G
| #10: Protein | Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P15825 |
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-Non-polymers , 7 types, 7982 molecules 












| #33: Chemical | ChemComp-MG / #34: Chemical | #35: Chemical | ChemComp-NA / #36: Chemical | ChemComp-CL / #37: Chemical | ChemComp-SR / #38: Chemical | ChemComp-CD / #39: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION |
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Sample preparation
| Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.27 % |
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-Data collection
| Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
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| Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2004 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
| Reflection | Resolution: 2.2→50 Å / Num. obs: 893114 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.95 % / Net I/σ(I): 18.2 |
| Reflection shell | Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 1.1 / % possible all: 99.5 |
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Processing
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| Refinement | Method to determine structure: FOURIER SYNTHESISStarting model: pdb entry 1S72 Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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| Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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| Refine LS restraints |
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About Yorodumi



Haloarcula marismortui (Halophile)
X-RAY DIFFRACTION
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