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Yorodumi- PDB-3cpw: The structure of the antibiotic LINEZOLID bound to the large ribo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cpw | ||||||
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Title | The structure of the antibiotic LINEZOLID bound to the large ribosomal subunit of HALOARCULA MARISMORTUI | ||||||
Components |
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Keywords | RIBOSOME / LINEZOLID / 50S RIBOSOMAL SUBUNIT / ANTIBIOTIC COMPLEXES / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Metal-binding / Zinc-finger | ||||||
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 / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / nucleotide binding / DNA repair / mRNA binding / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | HALOARCULA MARISMORTUI (Halophile) Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å | ||||||
Authors | Ippolito, J.A. / Kanyo, Z.K. / Wang, D. / Franceschi, F.J. / Moore, P.B. / Steitz, T.A. / Duffy, E.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Crystal Structure of the Oxazolidinone Antibiotic Linezolid Bound to the 50S Ribosomal Subunit Authors: Ippolito, J.A. / Kanyo, Z.K. / Wang, D. / Franceschi, F.J. / Moore, P.B. / Steitz, T.A. / Duffy, E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cpw.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3cpw.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 3cpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/3cpw ftp://data.pdbj.org/pub/pdb/validation_reports/cp/3cpw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 3 types, 3 molecules 094
#1: RNA chain | Mass: 946017.375 Da / Num. of mol.: 1 / Mutation: G2099A / Source method: isolated from a natural source / Source: (natural) HALOARCULA MARISMORTUI (Halophile) / Strain: DT41 / 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) / Strain: DT41 / References: GenBank: 3377779 |
#31: RNA chain | Mass: 1041.786 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (natural) Haloarcula marismortui (Halophile) / Strain: DT41 |
+50S ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ12
-Non-polymers , 9 types, 8068 molecules
#32: Chemical | ChemComp-ZLD / | ||||||||||||||
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#33: Chemical | ChemComp-MG / #34: Chemical | #35: Chemical | ChemComp-NA / #36: Chemical | ChemComp-CL / #37: Chemical | ChemComp-SR / #38: Chemical | ChemComp-CD / #39: Chemical | ChemComp-ACE / | #40: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.52 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG6000, KCL, NH4CL, MGCl2, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 1080057 / Num. obs: 470299 / % possible obs: 95.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.054 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.3 / Num. unique all: 41142 / % possible all: 84.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→40 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
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Refine LS restraints |
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