+Open data
-Basic information
Entry | Database: PDB / ID: 1me1 | ||||||||||||||||||||
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Title | Chimeric hairpin with 2',5'-linked RNA loop and RNA stem | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / Hairpin / (2' / 5')-RNA | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Authors | Denisov, A.Y. / Hannoush, R.N. / Gehring, K. / Damha, M.J. | Citation | Journal: J.AM.CHEM.SOC. / Year: 2003 | Title: A Novel RNA Motif Based on the Structure of Unusually Stable 2',5'-Linked r(UUCG) Loops Authors: Denisov, A.Y. / Hannoush, R.N. / Gehring, K. / Damha, M.J. History |
Remark 400 | COMPOUND NUCLOTIDES 5(U25), 6(U25), 7(C25), 8(5GP) HAS A NON-STANDARD 2'-5' LINKAGE. | |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1me1.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1me1.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 1me1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1me1_validation.pdf.gz | 322.6 KB | Display | wwPDB validaton report |
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Full document | 1me1_full_validation.pdf.gz | 368.5 KB | Display | |
Data in XML | 1me1_validation.xml.gz | 4.7 KB | Display | |
Data in CIF | 1me1_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1me1 ftp://data.pdbj.org/pub/pdb/validation_reports/me/1me1 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 3804.296 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: Structure was determined using standard 2D homo- and heteronuclear techniques: 2D-NOESY, DQF-COSY, TOCSY, H,C-HMQC, H,P-HetCOSY |
-Sample preparation
Details | Contents: 1.5 mM hairpin / Solvent system: D2O, H2O/D2O |
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Sample conditions | pH: 7 / Pressure: 1 atm / Temperature: 288 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Structures were refined by NMR-restrained molecular dynamics (12 ps, 300-1000 K) with final energy minimization | ||||||||||||
NMR representative | Selection criteria: closest to the average, lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY Conformers calculated total number: 20 / Conformers submitted total number: 10 |