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Yorodumi- PDB-2zjr: Refined native structure of the large ribosomal subunit (50S) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zjr | ||||||
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Title | Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans | ||||||
Components |
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Keywords | RIBOSOME / large ribosomal subunit / 50S / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / Methylation / Metal-binding / Zinc-finger | ||||||
Function / homology | Function and homology information large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Harms, J.M. / Wilson, D.N. / Schluenzen, F. / Connell, S.R. / Stachelhaus, T. / Zaborowska, Z. / Spahn, C.M.T. / Fucini, P. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Authors: Harms, J.M. / Wilson, D.N. / Schluenzen, F. / Connell, S.R. / Stachelhaus, T. / Zaborowska, Z. / Spahn, C.M. / Fucini, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zjr.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2zjr.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 2zjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zjr_validation.pdf.gz | 765 KB | Display | wwPDB validaton report |
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Full document | 2zjr_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2zjr_validation.xml.gz | 292 KB | Display | |
Data in CIF | 2zjr_validation.cif.gz | 402.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/2zjr ftp://data.pdbj.org/pub/pdb/validation_reports/zj/2zjr | HTTPS FTP |
-Related structure data
Related structure data | 2zjpC 2zjqC 3cf5C 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
-RNA chain , 2 types, 2 molecules XY
#1: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: PDB-2ZJQ |
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#2: RNA chain | Mass: 39605.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / References: PDB-2ZJQ |
+50S ribosomal protein ... , 28 types, 28 molecules ABCDEFGHIJKLMNOPQRSTUVWZ1234
-Non-polymers , 1 types, 35 molecules
#31: Chemical | ChemComp-MG / |
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-Details
Sequence details | THE SEQUENCE OF THE CHAIN X (RRNA-23S) MATCHES TO RESIDUES 2587937 - 2590816 IN GENEBANK WITH ...THE SEQUENCE OF THE CHAIN X (RRNA-23S) MATCHES TO RESIDUES 2587937 - 2590816 IN GENEBANK WITH ACCESSION 11612676. THE SEQUENCE OF THE CHAIN Y (RRNA-5S) MATCHES TO RESIDUES 254392 - 254514 IN GENEBANK WITH ACCESSION 11612676. |
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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: 4.42 Å3/Da / Density % sol: 72.17 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.91→29.91 Å / Num. all: 524780 / Num. obs: 493787 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 55.4 Å2 |
Reflection shell | Resolution: 2.91→3.04 Å / Num. unique all: 65279 / % possible all: 73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NKW Resolution: 2.91→29.9 Å
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→29.9 Å
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LS refinement shell | Resolution: 2.91→3.04 Å / Rfactor Rfree error: 0.007
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