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Open data
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Basic information
Entry | Database: PDB / ID: 2et4 | ||||||||||||||||||
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Title | Complex Between Neomycin B and the 16S-RRNA A-Site | ||||||||||||||||||
![]() | 5'-R(*![]() RNA / RNA-AMINOGLYCOSIDE INTERACTIONS / A SITE / UOU PAIRS / AA BULGES | Function / homology | NEOMYCIN / RNA / RNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Westhof, E. | ![]() ![]() Title: Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Authors: Francois, B. / Russell, R.J. / Murray, J.B. / Aboul-ela, F. / Masquida, B. / 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 | ![]() | 36.7 KB | Display | ![]() |
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PDB format | ![]() | 25.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2esiC ![]() 2esjC ![]() 2et3C ![]() 2et5C ![]() 2et8C ![]() 1j7tS S: Starting model for refinement C: citing same article ( |
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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 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.57 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: MPD, NACL, MGSO4, GLYCEROL, NA CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 7300 / Num. obs: 7300 / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry: 1J7T Resolution: 2.4→30 Å / σ(F): 1.5 Stereochemistry target values: G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY,A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERSFOR THE REFINEMENT OF NUCLEIC ACID CONTAINING STRUCTURES, ACTA CRYST. D, 52,57-64 (1996)
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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