+Open data
-Basic information
Entry | Database: PDB / ID: 2et3 | ||||||||||||||||||
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Title | Complex Between Gentamicin C1A and the 16S-RRNA A-Site | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / RNA-AMINOGLYCOSIDE INTERACTIONS / A SITE / UOU PAIRS / AA BULGES | Function / homology | Chem-LLL / RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | Authors | Westhof, E. | Citation | Journal: Nucleic Acids Res. / Year: 2005 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2et3.cif.gz | 35.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2et3.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 2et3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2et3_validation.pdf.gz | 998.9 KB | Display | wwPDB validaton report |
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Full document | 2et3_full_validation.pdf.gz | 1004 KB | Display | |
Data in XML | 2et3_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 2et3_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/2et3 ftp://data.pdbj.org/pub/pdb/validation_reports/et/2et3 | HTTPS FTP |
-Related structure data
Related structure data | 2esiC 2esjC 2et4C 2et5C 2et8C 1j7tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.99 % | ||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.936 Å |
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: 2.8→50 Å / Num. all: 4000 / Num. obs: 4000 / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1J7T Resolution: 2.8→20 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: 2.8→20 Å
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Refine LS restraints |
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