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Yorodumi- PDB-1qvg: Structure of CCA oligonucleotide bound to the tRNA binding sites ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qvg | ||||||
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Title | Structure of CCA oligonucleotide bound to the tRNA binding sites of the large ribosomal subunit of Haloarcula marismortui | ||||||
Components |
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Keywords | RIBOSOME / ribosome 50S / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX / PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.9 Å | ||||||
Authors | Schmeing, T.M. / Moore, P.B. / Steitz, T.A. | ||||||
Citation | Journal: RNA / Year: 2003 Title: Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit Authors: Schmeing, T.M. / Moore, P.B. / 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 | 1qvg.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1qvg.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1qvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/1qvg ftp://data.pdbj.org/pub/pdb/validation_reports/qv/1qvg | HTTPS FTP |
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-Related structure data
Related structure data | 1qvfC 1jj2S C: citing same article (ref.) 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
-RNA chain , 3 types, 5 molecules 09345
#1: RNA chain | Mass: 946034.375 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: 894.612 Da / Num. of mol.: 3 / Source method: obtained synthetically |
+50S ribosomal protein ... , 25 types, 25 molecules ABCDEFGIJKMNOPQRSTUVWXZ12
-Protein , 3 types, 3 molecules HLY
#11: Protein | Mass: 18022.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60617*PLUS |
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#15: Protein | Mass: 22856.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60618*PLUS |
#28: Protein | Mass: 8097.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: UniProt: P60619*PLUS |
-Non-polymers , 6 types, 7899 molecules
#32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-CD / #37: 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: 3.17 Å3/Da / Density % sol: 61.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.1 / Method: back-extraction, vapor diffusion / Details: Ban, N., (2000) Science, 289, 905. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9999 Å |
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Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 9, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 446294 / Num. obs: 443616 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.8→2.87 Å / Mean I/σ(I) obs: 2 / % possible all: 92.9 |
Reflection | *PLUS Highest resolution: 2.9 Å / % possible obs: 99.9 % / Num. measured all: 2687658 |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 2.97 Å / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1jj2 Resolution: 2.9→50 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.9 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.208 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |