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Yorodumi- PDB-1vqk: The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vqk | |||||||||
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Title | The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribosomal subunit of 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 information ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Haloarcula marismortui (Halophile) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | |||||||||
Authors | Schmeing, T.M. / Steitz, T.A. | |||||||||
Citation | Journal: Mol.Cell / Year: 2005 Title: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vqk.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1vqk.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1vqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vqk_validation.pdf.gz | 810.9 KB | Display | wwPDB validaton report |
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Full document | 1vqk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1vqk_validation.xml.gz | 314.9 KB | Display | |
Data in CIF | 1vqk_validation.cif.gz | 497.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/1vqk ftp://data.pdbj.org/pub/pdb/validation_reports/vq/1vqk | HTTPS FTP |
-Related structure data
Related structure data | 1vq4C 1vq5C 1vq8C 1vq9C 1vqlC 1vqmC 1vqoC 1vqpC 1s72S 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
-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: 1138.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CCdA-PHE-CAPROIC ACID BIOTIN 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, 7979 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.14 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1808 |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1808 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 797161 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Mean I/σ(I) obs: 1.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1S72 Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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