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- PDB-2uu9: Structure of the Thermus thermophilus 30S ribosomal subunit compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2uu9 | |||||||||
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Title | Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a Valine-ASL with cmo5U in position 34 bound to an mRNA with a GUG-codon in the A-site and paromomycin. | |||||||||
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Function / homology | ![]() small ribosomal subunit / cytosolic small ribosomal subunit / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Weixlbaumer, A. / Murphy, F.V. / Dziergowska, A. / Malkiewicz, A. / Vendeix, F.A.P. / Agris, P.F. / Ramakrishnan, V. | |||||||||
![]() | ![]() Title: Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Authors: Weixlbaumer, A. / Murphy 4th., F.V. / Dziergowska, A. / Malkiewicz, A. / Vendeix, F.A. / Agris, P.F. / Ramakrishnan, V. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2uuaC ![]() 2uubC ![]() 2uucC ![]() 1j5eS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-RNA chain , 3 types, 3 molecules AXY
#1: RNA chain | ![]() Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY. Source: (natural) ![]() ![]() ![]() |
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#22: RNA chain | ![]() Mass: 1610.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#23: RNA chain | ![]() Mass: 5490.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTU
#2: Protein | ![]() Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#3: Protein | ![]() Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#4: Protein | ![]() Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#5: Protein | ![]() Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#6: Protein | ![]() Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#7: Protein | ![]() Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#8: Protein | ![]() Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#9: Protein | ![]() Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#10: Protein | ![]() Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#11: Protein | ![]() Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#12: Protein | ![]() Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#13: Protein | ![]() Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#14: Protein | ![]() Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#15: Protein | ![]() Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#16: Protein | ![]() Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#17: Protein | ![]() Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#18: Protein | ![]() Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#19: Protein | ![]() Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#20: Protein | ![]() Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#21: Protein/peptide | ![]() Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Non-polymers , 4 types, 200 molecules ![](data/chem/img/PAR.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
#24: Chemical | ChemComp-PAR / ![]() | ||||
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#25: Chemical | ChemComp-MG / #26: Chemical | ChemComp-K / #27: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 74 % / Description: NONE |
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Crystal grow![]() | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 28, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.1→50 Å / Num. obs: 244079 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 3.1→3.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 92.9 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1J5E Resolution: 3.1→29.89 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 15215244.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: DENSITY WHICH IS BELIEVED TO BE NONE SPECIFICALLY BOUND ASL WAS NOT MODELED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.8642 Å2 / ksol: 0.280411 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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