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- PDB-2m24: NMR solution structure of the d3'-hairpin including the exon bind... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2m24 | |||||||||
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Title | NMR solution structure of the d3'-hairpin including the exon binding site 1 (EBS1) of the group II intron Sc.ai5gamma | |||||||||
![]() | RNA (29-MER) | |||||||||
![]() | RNA / group II intron / ribozyme / splicing / EBS1 / hairpin | |||||||||
Function / homology | RNA / RNA (> 10)![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | SOLUTION NMR / molecular dynamics, torsion angle dynamics | |||||||||
Model details | lowest energy, model1 | |||||||||
![]() | Kruschel, D. / Skilandat, M. / Sigel, R.K.O. | |||||||||
![]() | ![]() Title: NMR structure of the 5' splice site in the group IIB intron Sc.ai5 gamma--conformational requirements for exon-intron recognition. Authors: Kruschel, D. / Skilandat, M. / Sigel, R.K. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 351 KB | Display | ![]() |
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PDB format | ![]() | 295.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 331.9 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 9301.547 Da / Num. of mol.: 1 / Fragment: d3'EBS1 / Mutation: A15C, A17C / Source method: obtained synthetically Details: the sequence was produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-polymerase Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: molecular dynamics, torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 28 / NA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 29 / NA delta-angle constraints total count: 16 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 16 / NA other-angle constraints total count: 27 / NA sugar pucker constraints total count: 48 / NOE constraints total: 511 / NOE intraresidue total count: 176 / NOE sequential total count: 250 / Hydrogen bond constraints total count: 45 | ||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.2 Å |