+Open data
-Basic information
Entry | Database: PDB / ID: 486d | ||||||
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Title | X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES | ||||||
Components |
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Keywords | RIBOSOME / FUNCTIONAL MODELS OF 70S RIBOSOME / TRNA | ||||||
Function / homology | : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) Saccharomyces cerevisiae (brewer's yeast) Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING / Resolution: 7.5 Å | ||||||
Authors | Cate, J.H. / Yusupov, M.M. / Yusupova, G.Zh. / Earnest, T.N. / Noller, H.F. | ||||||
Citation | Journal: Science / Year: 1999 Title: X-ray crystal structures of 70S ribosome functional complexes. Authors: Cate, J.H. / Yusupov, M.M. / Yusupova, G.Z. / Earnest, T.N. / Noller, H.F. #1: Journal: Science / Year: 1999 Title: Identification of an RNA-Protein Bridge Spanning the Ribosomal Subunit Interface Authors: Culver, G.M. / Cate, J.H. / Yusupova, G.Z. / Yusupov, M.M. / Noller, H.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 486d.cif.gz | 138.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb486d.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 486d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/86/486d ftp://data.pdbj.org/pub/pdb/validation_reports/86/486d | HTTPS FTP |
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-Related structure data
Related structure data | 1gidS 1pbrS 3traS 430dS 4tnaS 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 , 7 types, 7 molecules ABCDEFG
#1: RNA chain | Mass: 24158.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 873.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE FROM T. THERMOPHILUS |
#3: RNA chain | Mass: 23328.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
#4: RNA chain | Mass: 911.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE FROM T. THERMOPHILUS |
#5: RNA chain | Mass: 23241.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
#6: RNA chain | Mass: 27506.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
#7: RNA chain | Mass: 10710.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) |
-Non-polymers , 1 types, 4 molecules
#8: Chemical | ChemComp-IR / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal grow | *PLUS Method: vapor diffusion, hanging, sitting drop / pH: 7.4 | ||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1051, 1.1055, 1.0764, 1.1047 | |||||||||||||||
Detector | Detector: AREA DETECTOR | |||||||||||||||
Radiation | Monochromator: SI(111) DOUBLE-CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Highest resolution: 7.5 Å / Num. all: 124437 / Num. obs: 124437 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 15.8 | |||||||||||||||
Reflection | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: MAD PHASING Starting model: 4TNA, 3TRA, 1PBR, 1GID, 430D Highest resolution: 7.5 Å Details: THE MODEL WAS BULIT BY MANUAL FITTING OF INDIVIDUAL RNA MOLECULES INTO THE EXPERIMENTAL ELECTRON DENSITY USING THE GRAPHIC PROGRAM O. P TRNA WAS BUILT FROM 3TRA (ALL BUT ANTICODON STEM-LOOP) ...Details: THE MODEL WAS BULIT BY MANUAL FITTING OF INDIVIDUAL RNA MOLECULES INTO THE EXPERIMENTAL ELECTRON DENSITY USING THE GRAPHIC PROGRAM O. P TRNA WAS BUILT FROM 3TRA (ALL BUT ANTICODON STEM-LOOP) AND 4TRNA (ANTICODON STEM-LOOP), A TRNA WAS BUILT FROM 3TRA (ANTICODON STEM-LOOP) AND 4TRNA (ALL BUT ANTICODON STEM-LOOP). THE P CODON WAS BASED ON A-RNA, THE A-SITE CODON ON 3TRA. BOTH FRAGMENTS OF 16S RRNA (MOLECULES 6 AND 7) WERE BASED ON 1GID, 1PBR, 430D, AND A-RNA
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Refinement step | Cycle: LAST / Highest resolution: 7.5 Å
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Refinement | *PLUS Highest resolution: 7.5 Å | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |