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Yorodumi- PDB-1fg0: LARGE RIBOSOMAL SUBUNIT COMPLEXED WITH A 13 BP MINIHELIX-PUROMYCI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fg0 | ||||||
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Title | LARGE RIBOSOMAL SUBUNIT COMPLEXED WITH A 13 BP MINIHELIX-PUROMYCIN COMPOUND | ||||||
Components |
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Keywords | RIBOSOME / ribosome assembly / RNA-RNA / ribozyme / A-site | ||||||
Function / homology | : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Haloarcula marismortui (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A. | ||||||
Citation | Journal: Science / Year: 2000 Title: The structural basis of ribosome activity in peptide bond synthesis. Authors: Nissen, P. / Hansen, J. / Ban, N. / Moore, P.B. / Steitz, T.A. #1: Journal: Science / Year: 2000 Title: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution Authors: Ban, N / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A. #2: Journal: Nature / Year: 1999 Title: Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit Authors: Ban, N. / Nissen, P. / Hansen, J. / Capel, M. / 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 | 1fg0.cif.gz | 281.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fg0.ent.gz | 210.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fg0_validation.pdf.gz | 386 KB | Display | wwPDB validaton report |
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Full document | 1fg0_full_validation.pdf.gz | 465.1 KB | Display | |
Data in XML | 1fg0_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1fg0_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/1fg0 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/1fg0 | HTTPS FTP |
-Related 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: 194851.688 Da / Num. of mol.: 1 / Fragment: DOMAIN V OF 23S RIBOSOMAL RNA / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
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#2: RNA chain | Mass: 11138.852 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THIS 13 BP MINIHELIX MIMICS A TYROSYL-TRNA ACCEPTOR STEM |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 292 K / Method: back-extraction, vapor diffusion / pH: 5.8 Details: PEG 6000, KCl, NH4Cl, potassium acetate, MgCl2, CdCl2, Tris-MES. Complex was obtained by crystal soaking in 0.1 mM minihelix-Puromycin, pH 5.8, Back-extraction, vapor diffusion, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions |
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Crystal grow | *PLUS pH: 7.1 / Method: unknown / Details: Ban, N., (2000) Science, 289, 905. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 13, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→70 Å / Num. all: 447121 / Num. obs: 447121 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 3.02→3.08 Å / Redundancy: 6 % / Rmerge(I) obs: 0.72 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 2712813 |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Resolution: 3→70 Å / σ(F): 0 / σ(I): 0 Details: The structure has been fitted to a 3.0 A resolution experimental map obtained by density modification using heavy atom derived phases and 2Fo(complex)-Fo(parent) amplitudes
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Refinement step | Cycle: LAST / Resolution: 3→70 Å
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Refinement | *PLUS Lowest resolution: 70 Å / σ(F): 0 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |