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Yorodumi- PDB-1q7y: Crystal Structure of CCdAP-Puromycin bound at the Peptidyl transf... -
+Open data
-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 | ||||||
Components |
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Keywords | RIBOSOME / ribosome 50S / puromycin / peptidyl transferase reaction / 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 / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Hansen, J.L. / Schmeing, T.M. / Moore, P.B. / Steitz, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q7y.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1q7y.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1q7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/1q7y ftp://data.pdbj.org/pub/pdb/validation_reports/q7/1q7y | HTTPS FTP |
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-Related structure data
Related structure data | 1m90C 1q81C 1q82C 1q86C 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 , 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) 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 |
-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) Haloarcula marismortui (Halophile) / References: UniProt: P15825 |
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#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 |
#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 , 8 types, 8105 molecules
#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: 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 | 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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