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- PDB-2uxd: Crystal structure of an extended tRNA anticodon stem loop in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2uxd | |||||||||
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Title | Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA CGGG in the context of the Thermus thermophilus 30S subunit. | |||||||||
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![]() | RIBOSOME / RIBONUCLEOPROTEIN / 30S RIBOSOMAL SUBUNIT / FRAMESHIFT SUPPRESSOR TRNA / TRNA / MRNA / CODON / A SITE / DECODING / METAL-BINDING / MESSENGER RNA / RIBOSOMAL PROTEIN / RNA-BINDING / PAROMOMYCIN / ANTICODON / STEM-LOOP / FRAMESHIFT / ZINC-FINGER / RRNA-BINDING / TRNA-BINDING / TRANSFER RNA | |||||||||
Function / homology | ![]() ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Dunham, C.M. / Selmer, M. / Phelps, S.S. / Kelley, A.C. / Suzuki, T. / Joseph, S. / Ramakrishnan, V. | |||||||||
![]() | ![]() Title: Structures of Trnas with an Expanded Anticodon Loop in the Decoding Center of the 30S Ribosomal Subunit. Authors: Dunham, C.M. / Selmer, M. / Phelps, S.S. / Kelley, A.C. / Suzuki, T. / Joseph, S. / 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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 940.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 161.9 KB | Display | |
Data in CIF | ![]() | 228.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 494287.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CHAIN A (16S RNA) HAS E. COLI NUMBERING / Source: (natural) ![]() ![]() |
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#22: RNA chain | Mass: 1295.842 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SEQUENCE BASED ON E.COLI TRNAPHE WITH ANTICODON SUBSTITUTED WITH CCCG Source: (synth.) synthetic construct (others) |
#23: RNA chain | Mass: 5723.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#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: 14429.661 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: 12324.670 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: 11722.116 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, 81 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: 4.17 Å3/Da / Density % sol: 70.5 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, AMMONIUM CHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM ACETATE, MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 228883 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 5.54 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.07 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 3.2→49.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 12576316.88 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 90.7949 Å2 / ksol: 0.306126 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→49.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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