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- PDB-1f9l: Solution Structure of a 22-Nucleotide Hairpin Similar to the P5AB... -
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Open data
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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 | |||||||||||||||||||||||
![]() | 5'-R(*![]() RNA / GA mismatches / GAAA tetraloop / metal-ion binding / Cobalt(III)hexammine / hairpin / P5abc / group I intron | Function / homology | RNA / RNA (> 10) | ![]() Method | SOLUTION NMR / restrained molecular dynamics, | Model type details | minimized average | ![]() Rudisser, S. / Tinoco Jr., I. | ![]() ![]() 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: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 22.1 KB | Display | ![]() |
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PDB format | ![]() | 14.2 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 290.9 KB | Display | ![]() |
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Full document | ![]() | 290.7 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 2.1 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: 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. |
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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 |