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Yorodumi- PDB-1k5i: NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k5i | ||||||||||||||||||
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Title | NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop | ||||||||||||||||||
Components | 5'-R(P*Keywords | RNA / CUCAA pentaloop / RNA hairpin / non standard base-base interaction | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / Distance Geometry, Simulated Annealing, Restrained Molecular Dynamics | Authors | Nagaswamy, U. / Gao, X. / Martinis, S.A. / Fox, G.E. | Citation | Journal: Nucleic Acids Res. / Year: 2001 | Title: NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop. Authors: Nagaswamy, U. / Gao, X. / Martinis, S.A. / Fox, G.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k5i.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k5i.ent.gz | 126 KB | Display | PDB format |
PDBx/mmJSON format | 1k5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k5i ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k5i | 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: 7369.440 Da / Num. of mol.: 1 / Fragment: 16S ribosomal RNA fragment (612-628) / Source method: obtained synthetically Details: The oligonucleotide was synthesized by T7 run-off transcription. |
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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 | Ionic strength: 10 mM Sodium Phosphate / pH: 6.5 / Pressure: ambient / Temperature: 298 K | |||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz |
-Processing
NMR software | Name: X-PLOR / Version: 3.1 / Developer: Brunger / Classification: refinement |
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Refinement | Method: Distance Geometry, Simulated Annealing, Restrained Molecular Dynamics Software ordinal: 1 Details: A total of 300 structures were calculated using distance geometry utilizing 123 experimentally derived distance restraints for the loop and 918 (258-experimental distances, 660-A form ...Details: A total of 300 structures were calculated using distance geometry utilizing 123 experimentally derived distance restraints for the loop and 918 (258-experimental distances, 660-A form distances) distance restraints for the stem region and 143 dihedral angle restraints. Additionally, 50 distance restraints were used to maintain the Watson-Crick geometry of the base pairs in the stem region. Final refinement resulted in 10 lowest energy structures. |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 33 / Conformers submitted total number: 10 |