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Open data
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Basic information
Entry | Database: PDB / ID: 1byj | |||||||||
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Title | GENTAMICIN C1A A-SITE COMPLEX | |||||||||
![]() | RNA (16S RNA) | |||||||||
![]() | RNA / COMPLEX (AMINOGLYCOSIDE-RIBOSOMAL RNA) | |||||||||
Function / homology | Chem-GE1 / 3,5-DIAMINO-CYCLOHEXANOL / Chem-GE3 / RNA / RNA (> 10)![]() | |||||||||
Method | SOLUTION NMR / simulated annealing | |||||||||
![]() | Yoshizawa, S. / Fourmy, D. / Puglisi, J.D. | |||||||||
![]() | ![]() Title: Structural origins of gentamicin antibiotic action. Authors: Yoshizawa, S. / Fourmy, D. / Puglisi, J.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 788.8 KB | Display | ![]() |
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PDB format | ![]() | 575.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 379.5 KB | Display | ![]() |
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Full document | ![]() | 544.2 KB | Display | |
Data in XML | ![]() | 115.4 KB | Display | |
Data in CIF | ![]() | 141.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: RNA chain | Mass: 8656.185 Da / Num. of mol.: 1 / Fragment: DECODING REGION / Source method: obtained synthetically / Details: 16S RNA WAS CHEMICALLY SYNTHESIZED. |
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#2: Sugar | ChemComp-GE1 / |
#3: Chemical | ChemComp-GE2 / |
#4: Sugar | ChemComp-GE3 / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: A TOTAL OF 326 RNA, 7 GENTAMICIN AND 46 GENTAMICIN-RNA RESTRAINTS WERE USED. 111 EXPERIMENTAL DIHEDRAL RESTRAINTS WERE USED. FOR 38 THE FINAL STRUCTURES DEVIATIONS FROM EXPERIMENTAL RESTRAINTS ...Text: A TOTAL OF 326 RNA, 7 GENTAMICIN AND 46 GENTAMICIN-RNA RESTRAINTS WERE USED. 111 EXPERIMENTAL DIHEDRAL RESTRAINTS WERE USED. FOR 38 THE FINAL STRUCTURES DEVIATIONS FROM EXPERIMENTAL RESTRAINTS ARE: RMSD NMR DISTANCE RESTRAINTS (379) (A): 0.0249 (0.0002) RMSD NMR DIHEDRAL RESTRAINTS (111) (DEG): 0.0127 (0.0016) DEVIATIONS FROM DEALIZED GEOMETRY (CVFF FORCEFIELD) RMSD BONDS (A): 0.0260 ( 0.0000) RMSD ANGLES (DEG): 0.0621 (0.0001) RMSD IMPROPERS (DEG): 0.0485 ( 0.0025) HEAVY ATOM RMS DEVIATIONS OF AVERAGE, MINIMIZED STRUCTURE FROM BEST- FIT SUPERPOSITION OF THE 38 FINAL STRUCTURES RMSD ALL RNA + GENTAMICIN (A): 0.89 |
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Sample preparation
Sample conditions | Ionic strength: 10 mM SODIUM PHOSPHATE / pH: 6.4 / Temperature: 308 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 38 / Conformers submitted total number: 38 |