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- PDB-1fc8: NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GG... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fc8 | ||||||||||||||||||
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Title | NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC) | ||||||||||||||||||
![]() | 5'-R(*![]() RNA/DNA CHIMERA / 2'F-ARABINONUCLEIC ACID / RNA / DNA / HYBRID DUPLEX / HAIRPIN / RNA-DNA CHIMERA COMPLEX | Function / homology | DNA/RNA hybrid / DNA/RNA hybrid (> 10) | ![]() Method | SOLUTION NMR / Distance geometry, simulated annealing | ![]() Trempe, J.-F. / Gehring, K. | ![]() ![]() Title: NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes. Authors: Trempe, J.F. / Wilds, C.J. / Denisov, A.Y. / Pon, R.T. / Damha, M.J. / Gehring, K. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 47.1 KB | Display | ![]() |
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PDB format | ![]() | 28.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 316.6 KB | Display | ![]() |
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Full document | ![]() | 339 KB | Display | |
Data in XML | ![]() | 4.4 KB | Display | |
Data in CIF | ![]() | 5.1 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: DNA/RNA hybrid | Mass: 3790.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SOLID PHASE SYNTHESIS; PHOSPHORAMIDITE CHEMISTRY |
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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. |
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Sample preparation
Details |
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Sample conditions | Ionic strength: 0.066 / pH: 7.2 / Pressure: ambient / Temperature: 293 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: Distance geometry, simulated annealing / Software ordinal: 1 Details: SA at 15000K for 15 psec from random coordinates. Refinement from lower energy structure at 3000K fro 9 psec. 5 structures generated. Total of 305 restraints: 98 intraresidue NOE-derived ...Details: SA at 15000K for 15 psec from random coordinates. Refinement from lower energy structure at 3000K fro 9 psec. 5 structures generated. Total of 305 restraints: 98 intraresidue NOE-derived distance constraints, 94 sequential NOE-derived distance constraints, 3 long range NOE-derived distance constraints, 15 distance restraints from hydrogen bonds, 91 dihedral angle restraints, 4 planarity constraints for base pairs | ||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||
NMR ensemble | Conformer selection criteria: RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM Conformers calculated total number: 5 / Conformers submitted total number: 5 |