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- PDB-4b3s: Crystal structure of the 30S ribosome in complex with compound 37 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b3s | ||||||
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Title | Crystal structure of the 30S ribosome in complex with compound 37 | ||||||
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![]() | RIBOSOME / ANTIBIOTIC | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ng, C.L. / Lang, K. / Shcherbakov, D. / Matt, T. / Perez-Fernandez, D. / Patak, R. / Meyer, M. / Duscha, S. / Akbergenov, R. / Boukari, H. ...Ng, C.L. / Lang, K. / Shcherbakov, D. / Matt, T. / Perez-Fernandez, D. / Patak, R. / Meyer, M. / Duscha, S. / Akbergenov, R. / Boukari, H. / Freihofer, P. / Kudyba, I. / Reddy, M.S.K. / Nandurikar, R.S. / Ramakrishnan, V. / Vasella, A. / Bottger, E.C. | ||||||
![]() | ![]() Title: 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Authors: Perez-Fernandez, D. / Shcherbakov, D. / Matt, T. / Leong, N.C. / Kudyba, I. / Duscha, S. / Boukari, H. / Patak, R. / Dubakka, S.R. / Lang, K. / Meyer, M. / Akbergenov, R. / Freihofer, P. / ...Authors: Perez-Fernandez, D. / Shcherbakov, D. / Matt, T. / Leong, N.C. / Kudyba, I. / Duscha, S. / Boukari, H. / Patak, R. / Dubakka, S.R. / Lang, K. / Meyer, M. / Akbergenov, R. / Freihofer, P. / Vaddi, S. / Thommes, P. / Ramakrishnan, V. / Vasella, A. / 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 | ![]() | 1017.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4b3mC ![]() 4b3rC ![]() 4b3tC ![]() 1j5eS C: citing same article ( 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: 493652.156 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: 5161.143 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: 14637.384 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 , 4 types, 182 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/RPO.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/RPO.gif)
![](data/chem/img/ZN.gif)
#24: Chemical | ChemComp-MG / #25: Chemical | ChemComp-K / #26: Chemical | ChemComp-RPO / ( | #27: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.22 % Description: DATA WAS USED TO REFINE AGAINST THE MODEL WITHOUT ANY LIGANDS FROM PDB ID 1J5E STRUCTURE USING CNS. THE OBTAINED DIFFERENCE MAP WAS USED TO ANALYSE THE BINDING OF LIGAND RPO, MANUAL MODEL FITTING USING COOT. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 4% MPD, 75MM NH4CL, 200MM KCL, 15MM MAGNESIUM CHLORIDE, MES-KOH 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: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→40 Å / Num. obs: 240081 / % possible obs: 99.2 % / Observed criterion σ(I): 2.1 / Redundancy: 4 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.15→3.25 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1J5E Resolution: 3.15→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 45.1848 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.15→40 Å
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Refine LS restraints |
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Xplor file |
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