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Open data
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Basic information
Entry | Database: PDB / ID: 4aqy | ||||||
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Title | Structure of ribosome-apramycin complexes | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. ...Matt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. / Perez-Fernandez, D. / Vasella, A. / Ramakrishnan, V. / Schacht, J. / Bottger, E.C. | ||||||
![]() | ![]() Title: Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin. Authors: Matt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. / Perez-Fernandez, D. / Vasella, A. / Ramakrishnan, V. / ...Authors: Matt, T. / Ng, C.L. / Lang, K. / Sha, S.H. / Akbergenov, R. / Shcherbakov, D. / Meyer, M. / Duscha, S. / Xie, J. / Dubbaka, S.R. / Perez-Fernandez, D. / Vasella, A. / Ramakrishnan, V. / Schacht, J. / Bottger, E.C. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "LA" 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 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. |
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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 | ![]() 1j5eS ![]() 2jl7 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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1 |
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Unit cell |
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Components
-RNA chain , 3 types, 3 molecules AWZ
#1: RNA chain | ![]() Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
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#22: RNA chain | Mass: 1860.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#23: RNA chain | Mass: 4815.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-30S 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: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#5: Protein | ![]() Mass: 17452.221 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: 17919.775 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: 11823.772 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: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#15: Protein | ![]() Mass: 10447.213 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: 12193.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#18: Protein | ![]() Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() |
#19: Protein | ![]() Mass: 10474.269 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: 3218.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Non-polymers , 5 types, 226 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/AM2.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/AM2.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#24: Chemical | ChemComp-MG / #25: Chemical | ChemComp-K / #26: Chemical | ChemComp-AM2 / ![]() #27: Chemical | #28: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.83 Å3/Da / Density % sol: 74.31 % Description: 30S MODEL PDB CODE 1J5E WAS USED AS INITIAL MODEL SUBJECTED TO RIGID BODY REFINEMENT USING CNS. |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: MPD, NH4CL, KCL, CACL2, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Apr 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.5→40 Å / Num. obs: 178694 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1J5E Resolution: 3.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
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Solvent computation | Bsol: 72.0618 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.5→40 Å
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Refine LS restraints |
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Xplor file |
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