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Yorodumi- PDB-2ky2: The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ky2 | ||||||||||||||||||||
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Title | The Structure of RNA Internal Loops with Tandem AG Pairs: 5'UAGG/3'GGAU | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / tandem AG pairs / thermodynamics / imino AG pair / dual syn GG pair / extrahelical U | Function / homology | RNA | Function and homology information Method | SOLUTION NMR / simulated annealing | Model details | closest to the average, model 1 | Authors | Hammond, N.B. / Kennedy, S.D. / Turner, D.H. | Citation | Journal: Biochemistry / Year: 2010 | Title: RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA. Authors: Hammond, N.B. / Tolbert, B.S. / Kierzek, R. / Turner, D.H. / Kennedy, S.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ky2.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ky2.ent.gz | 97.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ky2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ky2_validation.pdf.gz | 324.9 KB | Display | wwPDB validaton report |
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Full document | 2ky2_full_validation.pdf.gz | 390.7 KB | Display | |
Data in XML | 2ky2_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 2ky2_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/2ky2 ftp://data.pdbj.org/pub/pdb/validation_reports/ky/2ky2 | HTTPS FTP |
-Related structure data
Related structure data | 2kxzC 2ky0C 2ky1C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 2910.807 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Tandem AG pairs with UG closing pairs: r(GGUAGGCCA)2 | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.1 / Pressure: ambient / Temperature: 274 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 40 / Conformers submitted total number: 10 |