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Yorodumi- PDB-2f87: Solution structure of a GAAG tetraloop in SRP RNA from Pyrococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f87 | ||||||
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Title | Solution structure of a GAAG tetraloop in SRP RNA from Pyrococcus furiosus | ||||||
Components | SRP RNA | ||||||
Keywords | RNA / SRP / GNRR | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model type details | minimized average | ||||||
Authors | Okada, K. / Takahashi, M. / Sakamoto, T. / Nakamura, K. / Kanai, A. / Kawai, G | ||||||
Citation | Journal: Nucleosides Nucleotides Nucleic Acids / Year: 2006 Title: Solution structure of a GAAG tetraloop in helix 6 of SRP RNA from Pyrococcus furiosus Authors: Okada, K. / Takahashi, M. / Sakamoto, T. / Kawai, G. / Nakamura, K. / Kanai, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f87.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f87.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 2f87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f87_validation.pdf.gz | 322.6 KB | Display | wwPDB validaton report |
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Full document | 2f87_full_validation.pdf.gz | 395.3 KB | Display | |
Data in XML | 2f87_validation.xml.gz | 4 KB | Display | |
Data in CIF | 2f87_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/2f87 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/2f87 | HTTPS FTP |
-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: 3906.400 Da / Num. of mol.: 1 / Fragment: pfHE6-12 / Source method: obtained synthetically Details: The RNA fragment, pfHE6-12 was chemically synthesized by a phosphoramidite method, using an automatic DNA/RNA synthesizer, Expedite model 8909 (PerSeptive Biosystems). |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D homonuclear techniques. |
-Sample preparation
Details | Contents: 2.0mM RNA Buffer Na; 95% H2O, 5% D2O; 2.0mM RNA; 20mM Phosphate Buffer Na; 100% D2O Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 50mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 283 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: The structure is based on a total of 179 restraints, 127 are NOE-derived distance constraints, 34 dihedral angle restraints, 18 distance restraints from hydrogen bonds. | |||||||||||||||
NMR representative | Selection criteria: minimized average structure | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 13 |