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- PDB-1q7y: Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transf... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q7y | ||||||
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Title | Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transferase center of the 50S ribosomal subunit | ||||||
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![]() | RIBOSOME / ribosome 50S / puromycin / peptidyl transferase reaction / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX / PROTEIN-RNA COMPLEX | ||||||
Function / homology | ![]() ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / DNA repair / nucleotide binding / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hansen, J.L. / Schmeing, T.M. / Moore, P.B. / Steitz, T.A. | ||||||
![]() | ![]() Title: Structural Insights Into Peptide Bond Formation Authors: Hansen, J.L. / Schmeing, T.M. / Moore, P.B. / Steitz, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.5 MB | Display | ![]() |
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PDB format | ![]() | 1.9 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1002.6 KB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 359.7 KB | Display | |
Data in CIF | ![]() | 558.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m90C ![]() 1q81C ![]() 1q82C ![]() 1q86C ![]() 1jj2S C: citing same article ( S: Starting model for refinement |
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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 , 2 types, 2 molecules AB
#1: RNA chain | Mass: 946034.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA/RNA hybrid , 1 types, 1 molecules 5
#3: DNA/RNA hybrid | Mass: 878.613 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CCdA-P-Puromycin synthesised by Michael Yarus Lab, Unviversity of Colorado at Boulder |
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+50S ribosomal protein ... , 24 types, 24 molecules CDEFGHKLMOPQRSTUVWXYZ234
-Protein , 4 types, 4 molecules IJN1
#10: Protein | Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#11: Protein | Mass: 18022.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 22856.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 8097.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 8 types, 8105 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PUY.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PUY.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-PO4 / | #37: Chemical | ChemComp-PUY / | #38: Chemical | ChemComp-CD / #39: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.14 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 6K, KCl, NaCl, MgCl2, NH4Cl, EG, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 100K | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 13, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 36.8 Å2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1JJ2 Resolution: 3.2→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 355423.95 / Data cutoff high rms absF: 355423.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.8395 Å2 / ksol: 0.264244 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.31 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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