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Yorodumi- PDB-1f9l: Solution Structure of a 22-Nucleotide Hairpin Similar to the P5AB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f9l | |||||||||||||||||||||||
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Title | Solution Structure of a 22-Nucleotide Hairpin Similar to the P5ABC Region of a Group I Ribozyme with Cobalt(III)hexammine Complexed to the GAAA Tetraloop | |||||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / GA mismatches / GAAA tetraloop / metal-ion binding / Cobalt(III)hexammine / hairpin / P5abc / group I intron | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / restrained molecular dynamics, | Model type details | minimized average | Authors | Rudisser, S. / Tinoco Jr., I. | Citation | Journal: J.Mol.Biol. / Year: 2000 | Title: Solution structure of Cobalt(III)hexammine complexed to the GAAA tetraloop, and metal-ion binding to G.A mismatches. Authors: Rudisser, S. / Tinoco Jr., I. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f9l.cif.gz | 20.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f9l.ent.gz | 14.6 KB | Display | PDB format |
PDBx/mmJSON format | 1f9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/1f9l ftp://data.pdbj.org/pub/pdb/validation_reports/f9/1f9l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 7175.371 Da / Num. of mol.: 1 / Fragment: P5ABC DOMAIN / Source method: obtained synthetically Details: The RNA was enzymatically synthesized from a synthetic RNA template using T7 RNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: The structure of the complex was determined using 7 NOE constraints between Cobalt(III)Hexammine and the GAAA tetraloop. In addition, the same constraints as for the 22-nucleotide hairpin ...Text: The structure of the complex was determined using 7 NOE constraints between Cobalt(III)Hexammine and the GAAA tetraloop. In addition, the same constraints as for the 22-nucleotide hairpin without Cobalt(III)hexammine were used. For RNA without Cobalt(III)Hexammine see entry 1EOR. |
-Sample preparation
Details | Contents: 2.8 mM RNA, 10 mM sodium Phosphate, 200 mM NaCl, 0.1 mM EDTA pH 5.6, 3.4 mM Cobalt(III)Hexammine Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 200 mM NaCl / pH: 5.6 / Pressure: ambient / Temperature: 283 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: restrained molecular dynamics, / Software ordinal: 1 Details: 356 NOE constraints, 16 sugar pucker constraints, 93 torsion angle constraints, 7 constraints between Cobalt(III)Hexammine and the GAAA tetraloop | ||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 1 |