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Yorodumi- PDB-1q86: Crystal structure of CCA-Phe-cap-biotin bound simultaneously at h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q86 | ||||||
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Title | Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit. | ||||||
Components |
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Keywords | RIBOSOME / Ribosome 50S / A-site / P-site / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX / PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information 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 | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 | 1q86.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1q86.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1q86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q86_validation.pdf.gz | 784.9 KB | Display | wwPDB validaton report |
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Full document | 1q86_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1q86_validation.xml.gz | 332.7 KB | Display | |
Data in CIF | 1q86_validation.cif.gz | 518.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/1q86 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/1q86 | HTTPS FTP |
-Related structure data
Related structure data | 1m90C 1q7yC 1q81C 1q82C 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, 4 molecules AB56
#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.: 2 / Source method: obtained synthetically Details: CC-phenylalanine-carpiotic acid biotin synthesised by Scott Strobel Lab Yale University. |
+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 , 7 types, 8104 molecules
#32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | #37: Chemical | ChemComp-CD / #38: 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: 3.18 Å3/Da / Density % sol: 61.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 | Detector: CCD |
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: 40.4 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JJ2 Resolution: 3→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 183922.96 / Data cutoff high rms absF: 183922.96 / 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: 37.5602 Å2 / ksol: 0.306789 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.11 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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