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Yorodumi- PDB-1feq: NMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A MO... -
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-Basic information
Entry | Database: PDB / ID: 1feq | ||||||||||||||||||
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Title | NMR SOLUTION STRUCTURE OF THE ANTICODON OF TRNA(LYS3) WITH T6A MODIFICATION AT POSITION 37 | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / TRNA / Anticodon STEM LOOP / TRNA DOMAIN / RNA HAIRPIN / T6A | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / global fold by distance geometry. Refinement by simulated annealing using the AMBER forcefield | Authors | Stuart, J.W. / Gdaniec, Z. / Guenther, R.H. / Marszalek, M. / Sochacka, E. / Malkiewicz, A. / Agris, P.F. | Citation | Journal: Biochemistry / Year: 2000 | Title: Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A. Authors: Stuart, J.W. / Gdaniec, Z. / Guenther, R. / Marszalek, M. / Sochacka, E. / Malkiewicz, A. / Agris, P.F. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 1feq.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1feq.ent.gz | 104.6 KB | Display | PDB format |
PDBx/mmJSON format | 1feq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/1feq ftp://data.pdbj.org/pub/pdb/validation_reports/fe/1feq | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 5510.319 Da / Num. of mol.: 1 Fragment: ANTICODON (RESIDUES 27-43) OF TRNA(LYS3) WITH T6A MODIFICATION AT POSITION 37 Source method: obtained synthetically Details: sequence of tRNA(Lys3) with terminal base pair replaced with GC to enhance synthesis yield and stability |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: This structure was determined using standard 2D homonuclear techniques |
-Sample preparation
Details | Contents: 1.2 mM RNA, 10 mM cacodylate buffer, pH 5.6, 0.1 mM EDTA Solvent system: 94% H2O, 6% D2O |
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Sample conditions | pH: 5.6 / Pressure: 1 atm / Temperature: 289 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: global fold by distance geometry. Refinement by simulated annealing using the AMBER forcefield Software ordinal: 1 Details: 272 restraints, 207 NOE-derived, 13 h-bond, 52 dihedral angle. Chi torsion was left unrestrained although likely anti for all residues. | ||||||||||||
NMR representative | Selection criteria: minimized average structure of family a (struct 2-5) | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 11 |