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Yorodumi- PDB-1yj9: Crystal Structure Of The Mutant 50S Ribosomal Subunit Of Haloarcu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yj9 | ||||||
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Title | Crystal Structure Of The Mutant 50S Ribosomal Subunit Of Haloarcula Marismortui Containing a three residue deletion in L22 | ||||||
Components |
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Keywords | RIBOSOME / L22 / deletion mutation / mutated 50S subunits | ||||||
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: 2.8 Å | ||||||
Authors | Tu, D. / Blaha, G. / Moore, P.B. / Steitz, T.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2005 Title: Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Authors: Tu, D. / Blaha, G. / Moore, P.B. / Steitz, T.A. | ||||||
History |
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Remark 2 | RESOLUTION. 2.90 ANGSTROMS. | ||||||
Remark 999 | SEQUENCE Sequence reference for this ribosome: Baliga, N.S., Bonneau, R., Facciotti, M.T., Pan, M., ...SEQUENCE Sequence reference for this ribosome: Baliga, N.S., Bonneau, R., Facciotti, M.T., Pan, M., Glusman, G., Deutsch, E.W., Shannon, P., Chiu, Y., Weng, R.S., Gan, R.R., et al.(2004). 999 'Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea.Genome Res. 14, 2221-2234. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yj9.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1yj9.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 1yj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/1yj9 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yj9 | HTTPS FTP |
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-Related structure data
Related structure data | 1yhqC 1yi2C 1yijC 1yitC 1yjnC 1yjwC 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
-RNA chain , 2 types, 2 molecules 09
#1: RNA chain | Mass: 946157.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: encoded by rrnA operon / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT50 / References: GenBank: 55229667 |
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#2: RNA chain | Mass: 39303.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT50 / References: GenBank: 3377778 |
+50S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules ABCDEFHIJKLMNOPQRSTUVWXYZ123
-Protein , 1 types, 1 molecules G
#9: Protein | Mass: 37213.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT50 / References: UniProt: P15825 |
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-Non-polymers , 6 types, 8015 molecules
#32: Chemical | ChemComp-MG / #33: Chemical | #34: Chemical | ChemComp-NA / #35: Chemical | ChemComp-CL / #36: Chemical | ChemComp-CD / #37: 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: 3.1 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 6000, KCl, NH4Cl, MgCl2, Kacetate, pH 5.8, VAPOR DIFFUSION, 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: ALS / Beamline: 8.2.2 / Wavelength: 1.08 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 392658 / Redundancy: 3 % / Biso Wilson estimate: 81.3 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2 / Num. unique all: 39036 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 419035.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: In refinement, all data available was used, i.e. including data that are weaker than I/sigma = 2.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.7575 Å2 / ksol: 0.292769 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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