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Yorodumi- PDB-1njm: The crystal structure of the 50S Large ribosomal subunit from Dei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1njm | ||||||
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Title | The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin | ||||||
Components |
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Keywords | RIBOSOME / Ribosomes / tRNA / puromycin / sparsomycin / peptidyl-transferase / peptide bond formation | ||||||
Function / homology | Function and homology information 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER MAPS / Resolution: 3.6 Å | ||||||
Authors | Bashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Hansen, H.A. / Yonath, A. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Structural basis of the ribosomal machinery for Peptide bond formation, translocation, and nascent chain progression Authors: Bashan, A. / Agmon, I. / Zarivatch, R. / Schluenzen, F. / Harms, J.M. / Berisio, R. / Bartels, H. / Franceschi, F. / Auerbach, T. / Hansen, H.A. / Kossoy, E. / Kessler, M. / Yonath, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1njm.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1njm.ent.gz | 1018.7 KB | Display | PDB format |
PDBx/mmJSON format | 1njm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1njm_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 1njm_full_validation.pdf.gz | 611 KB | Display | |
Data in XML | 1njm_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 1njm_validation.cif.gz | 86.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1njm ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1njm | HTTPS FTP |
-Related structure data
Related structure data | 1njnC 1njoC 1njpC 1nkwS 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
#1: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: GenBank: 6460405 |
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#2: RNA chain | Mass: 11391.945 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The terminal C of ASM was coupled via a phosphodiester bond to the 5 OH of the N6-dimethyl moiety of puromycin |
#3: Protein | Mass: 16125.997 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RXJ5 |
#4: Protein | Mass: 25415.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: UniProt: Q9RX88 |
#5: Chemical | ChemComp-SPS / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Details: ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusionDetails: Harms, J.M., (2001) Cell (Cambridge,Mass.), 107, 679. pH: 7.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Nov 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 290998 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Rsym value: 0.169 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.6→3.66 Å / Mean I/σ(I) obs: 1.7 / Rsym value: 0.356 / % possible all: 93.8 |
Reflection | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.169 |
Reflection shell | *PLUS % possible obs: 93.8 % / Rmerge(I) obs: 0.356 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER MAPS Starting model: PDB ENTRY 1NKW Resolution: 3.6→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 3.6→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.326 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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