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Yorodumi- PDB-3cme: The Structure of CA and CCA-PHE-CAP-BIO Bound to the Large Riboso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cme | |||||||||
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Title | The Structure of CA and CCA-PHE-CAP-BIO Bound to 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 / HYDROLYSIS OF PEPTIDYL-tRNA | |||||||||
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) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.95 Å | |||||||||
Authors | Simonovic, M. / Steitz, T.A. | |||||||||
Citation | Journal: Rna / Year: 2008 Title: Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA. Authors: Simonovic, M. / 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 | 3cme.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3cme.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 3cme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/3cme ftp://data.pdbj.org/pub/pdb/validation_reports/cm/3cme | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
+50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123
-RNA chain , 4 types, 4 molecules 0956
#30: RNA chain | Mass: 946463.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) |
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#31: RNA chain | Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 6468293 |
#32: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#33: RNA chain | Mass: 893.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 9 types, 8115 molecules
#34: Chemical | ChemComp-MG / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-SR / #37: Chemical | ChemComp-NA / #38: Chemical | ChemComp-CD / #39: Chemical | #40: Chemical | ChemComp-PHE / | #41: Chemical | ChemComp-ACA / | #42: 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: 3.04 Å3/Da / Density % sol: 59.49 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: PEG 6000, KCL, NH4CL, MGCL2, KACETATE, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||
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: 24-ID-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→70 Å / Num. all: 369334 / Num. obs: 369334 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.261 / Χ2: 1.369 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 7.1 % / Num. unique all: 36740 / Χ2: 0.768 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.95→49.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 49296.121 / 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: 45.044 Å2 / ksol: 0.302 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.95→49.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.08 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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