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Yorodumi- PDB-3cd6: Co-cystal of large Ribosomal Subunit mutant G2616A with CC-Puromycin -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cd6 | ||||||
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Title | Co-cystal of large Ribosomal Subunit mutant G2616A with CC-Puromycin | ||||||
Components |
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Keywords | RIBOSOME / G2616A mutation / 23S rRNA / large ribosomal subunit / CC-Puromycin | ||||||
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 / molecular replacement / Resolution: 2.75 Å | ||||||
Authors | Blaha, G. / Gurel, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. Authors: Blaha, G. / Gurel, G. / Schroeder, S.J. / 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 | 3cd6.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3cd6.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 3cd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/3cd6 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/3cd6 | HTTPS FTP |
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-Related structure data
Related structure data | 3cc2C 3cc4C 3cc7C 3cceC 3ccjC 3cclC 3ccmC 3ccqC 3ccrC 3ccsC 3ccuC 3ccvC C: citing same article (ref.) |
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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
+50S ribosomal protein ... , 29 types, 29 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ123
-RNA chain , 3 types, 3 molecules 094
#30: RNA chain | Mass: 946431.500 Da / Num. of mol.: 1 / Mutation: G2099A, G2616A / 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: 1098.880 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 7 types, 8113 molecules
#33: Chemical | ChemComp-MG / #34: Chemical | ChemComp-CL / #35: Chemical | ChemComp-SR / #36: Chemical | ChemComp-NA / #37: Chemical | ChemComp-CD / #38: Chemical | #39: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132, WITH G2099A AND ...THE SEQUENCE OF CHAIN 0 MATCHES TO GB ENTRY AY596297 BETWEEN 2634210 AND 2637132, WITH G2099A AND G2616A MUTATIONS. THE SEQUENCE OF CHAIN Z MATCHES TO REFSEQ ENTRY YP_136287. |
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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: 3.11 Å3/Da / Density % sol: 60.41 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: sitting drop / pH: 5.8 Details: PEG6000, KCL, NH4CL, MGCl2, pH 5.80, sitting 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: Oct 14, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→50 Å / Num. obs: 468902 / % possible obs: 99.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 72.9 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 13.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→49.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 94839.89 / 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: 40.6539 Å2 / ksol: 0.302133 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→49.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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