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- PDB-1mwl: Crystal structure of geneticin bound to the eubacterial 16S rRNA ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mwl | ||||||||||||||||||
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Title | Crystal structure of geneticin bound to the eubacterial 16S rRNA A site | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / AMINOGLYCOSIDE ANTIBIOTIC / GENETICIN-A-SITE COMPLEX / 16S RIBOSOMAL RNA / Bulged adenines / UoU pairs | Function / homology | GENETICIN / RNA / RNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Vicens, Q. / Westhof, E. | ![]() ![]() Title: Crystal structure of geneticin bound to a bacterial 16S ribosomal RNA A site oligonucleotide Authors: Vicens, Q. / Westhof, E. #1: ![]() Title: Crystal structure of a complex between the aminoglycoside tobramycin and an oligonucleotide containing the ribosomal decoding A site Authors: Vicens, Q. / Westhof, E. #2: ![]() Title: Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site Authors: Vicens, Q. / Westhof, E. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37 KB | Display | ![]() |
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PDB format | ![]() | 26.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1lc4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 7048.259 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: eubacterial 16S rRNA A site. The oligonucleotide contains two A sites. #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: MPD, MAGNESIUM SULPHATE, POTASSIUM CHLORIDE, SODIUM CHLORIDE, SODIUM CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
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 |
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Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.4→25 Å / Num. obs: 5466 / % possible obs: 88.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 65.5 Å2 / Rsym value: 0.062 / Net I/σ(I): 39.3 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 6.7 / Num. unique all: 566 / Rsym value: 0.211 / % possible all: 92.8 | ||||||||||||||||||
Reflection | *PLUS Num. measured all: 24145 / Rmerge(I) obs: 0.062 | ||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 92.8 % / Num. unique obs: 566 / Rmerge(I) obs: 0.211 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LC4 (RNA ONLY) Resolution: 2.4→22.61 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.5 Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New parameters for the refinement of nucleic acid containing structures, Acta Cryst, D, 52, 57-64 (1996)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.9452 Å2 / ksol: 0.314673 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→22.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.119 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.4 Å |