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Yorodumi- PDB-1ffk: CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ffk | ||||||
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Title | CRYSTAL STRUCTURE OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI AT 2.4 ANGSTROM RESOLUTION | ||||||
Components |
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Keywords | RIBOSOME / ribosome assembly / RNA-RNA / protein-RNA / protein-protein | ||||||
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 / Resolution: 2.4 Å | ||||||
Authors | Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A. | ||||||
Citation | 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. #1: 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. #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. #3: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: A 9 A resolution X-ray crystallographic map of the large ribosomal subunit Authors: Ban, N. / Freeborn, B. / Nissen, P. / Penczek, P. / Grasucci, R.A. / Sweet, R. / Frank, J. / 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 | 1ffk.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1ffk.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 1ffk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/1ffk ftp://data.pdbj.org/pub/pdb/validation_reports/ff/1ffk | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 946034.375 Da / Num. of mol.: 1 / 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: 39318.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CULTURED CELLS / Source: (natural) Haloarcula marismortui (Halophile) / References: GenBank: 3377779 |
+RIBOSOMAL PROTEIN ... , 27 types, 27 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZ1
-Non-polymers , 4 types, 13 molecules
#30: Chemical | ChemComp-K / | ||||
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#31: Chemical | #32: Chemical | ChemComp-CD / #33: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: backextraction, vapor diffusion / pH: 5.8 Details: PEG 6000, KCl, NH4Cl, MgCl2, CdCl2, potassium acetate, Tris-MES, pH 5.8, backextraction, vapor diffusion, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.1 / Method: back-extraction, vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→90 Å / Num. all: 666819 / Num. obs: 666819 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.6 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.691 / Num. unique all: 50941 / % possible all: 73.5 | |||||||||||||||
Reflection | *PLUS Num. measured all: 6089802 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 71 % / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.4→90 Å / Cross valid method: THROUGHOUT / σ(F): 2 Stereochemistry target values: Engh & Huber, Parkinson et al. Details: Real-space refinement in TNT against experimental map followed by phase-restrained refinement in CNS
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.4→90 Å
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Refine LS restraints |
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Software | *PLUS Name: 'TNT & CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 90 Å / σ(F): 2 / % reflection Rfree: 1 % / Rfactor obs: 0.252 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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