+Open data
-Basic information
Entry | Database: PDB / ID: 1f5h | |||||||||||||||||||||||
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Title | The G7(syn)-G4(anti) structure of r(GCAGGCGUGC)2 | |||||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / GUANINE-GUANINE / GG MISMATCH / CONFORMATIONAL EXCHANGE / BASE FLIPPING / syn GLYCOSIDIC TORSION | Function / homology | RNA | Function and homology information Method | SOLUTION NMR / Simulated annealing; Energy minimization | Model type details | minimized average | Authors | Burkard, M.E. / Turner, D.H. | Citation | Journal: Biochemistry / Year: 2000 Title: NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs Authors: Burkard, M.E. / Turner, D.H. #1: Journal: Biochemistry / Year: 1999 Title: Thermodyamics of single mismatches in RNA duplexes Authors: Kierzek, R. / Burkard, M.E. / Turner, D.H. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f5h.cif.gz | 327.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f5h.ent.gz | 275 KB | Display | PDB format |
PDBx/mmJSON format | 1f5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f5h_validation.pdf.gz | 336 KB | Display | wwPDB validaton report |
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Full document | 1f5h_full_validation.pdf.gz | 562.3 KB | Display | |
Data in XML | 1f5h_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1f5h_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f5h ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f5h | 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: 3231.988 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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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: 80 mM NaCl; 10 mM phosphate, pH 7 / Solvent system: D2O |
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Sample conditions | Ionic strength: 80 mM / pH: 7 / Pressure: ambient / Temperature: 310.15 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: Simulated annealing; Energy minimization / Software ordinal: 1 Details: The structures are based on 88 NOE distance restraints, 11 hydrogen-bond restraints for Watson-Crick pairs, and loosely restrained torsion angles. 22 of 25 structures were used to generate ...Details: The structures are based on 88 NOE distance restraints, 11 hydrogen-bond restraints for Watson-Crick pairs, and loosely restrained torsion angles. 22 of 25 structures were used to generate the minimized, averaged structure. G4 was restrained to the syn glycosidic conformation | ||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy. First model represents the minimized averaged structure Conformers calculated total number: 40 / Conformers submitted total number: 26 |