+Open data
-Basic information
Entry | Database: PDB / ID: 2m5u | ||||||||||||||||||||
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Title | NMR structure of the P4 hairpin of the CPEB3 ribozyme | ||||||||||||||||||||
Components | RNA_(5'-R(*Keywords | RNA / CPEB3 / UGGU tetraloop / ribozyme / hairpin | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / molecular dynamics | Model details | lowest energy, model1 | Authors | Skilandat, M. / Rowinska-Zyrek, M. / Sigel, R.K.O. | Citation | Journal: J.Biol.Inorg.Chem. / Year: 2014 | Title: Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain. Authors: Skilandat, M. / Rowinska-Zyrek, M. / Sigel, R.K. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m5u.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m5u.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 2m5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m5u_validation.pdf.gz | 418.6 KB | Display | wwPDB validaton report |
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Full document | 2m5u_full_validation.pdf.gz | 493.5 KB | Display | |
Data in XML | 2m5u_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2m5u_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/2m5u ftp://data.pdbj.org/pub/pdb/validation_reports/m5/2m5u | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 7051.210 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The sequence was produced by in-vitro transcription from a synthetic dsDNA template using T7 RNA-Polymerase. |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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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 / Software ordinal: 1 | ||||||||||||||||||||||||||||||||
NMR constraints | NA alpha-angle constraints total count: 17 / NA beta-angle constraints total count: 16 / NA chi-angle constraints total count: 21 / NA delta-angle constraints total count: 18 / NA epsilon-angle constraints total count: 16 / NA gamma-angle constraints total count: 16 / NOE constraints total: 449 / NOE intraresidue total count: 145 / NOE sequential total count: 247 / Hydrogen bond constraints total count: 46 | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 150 / Conformers submitted total number: 15 |