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Yorodumi- PDB-1kos: SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kos | ||||||||||||||||||
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Title | SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM LOOP CONTAINING RIBOTHYMIDINE AT ITS NATURALLY OCCURRING POSITION | ||||||||||||||||||
Components | 5'-R(*Keywords | RNA / TRNA / T STEM LOOP / TRNA DOMAIN / RNA HAIRPIN / RNA FOLDING | Function / homology | RNA / RNA (> 10) | Function and homology information Method | SOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING | Authors | Koshlap, K.M. / Guenther, R. / Sochacka, E. / Malkiewicz, A. / Agris, P.F. | Citation | Journal: Biochemistry / Year: 1999 Title: A distinctive RNA fold: the solution structure of an analogue of the yeast tRNAPhe T Psi C domain. Authors: Koshlap, K.M. / Guenther, R. / Sochacka, E. / Malkiewicz, A. / Agris, P.F. #1: Journal: Biopolymers / Year: 1998 Title: Small Structural Ensembles for a 17-Nucleotide Mimic of the tRNA Tpsic-Loop Via Fitting Dipolar Relaxation Rates with the Quadratic Programming Algorithm Authors: Schmitz, U. / Donati, A. / James, T.L. / Ulyanov, N.B. / Yao, L. #2: Journal: J.Biomol.NMR / Year: 1997 Title: The Dynamic NMR Structure of the T Psi C-Loop: Implications for the Specificity of tRNA Methylation Authors: Yao, L.J. / James, T.L. / Kealey, J.T. / Santi, D.V. / Schmitz, U. #3: Journal: Biochemistry / Year: 1986 Title: Restrained Refinement of the Monoclinic Form of Yeast Phenylalanine Transfer RNA. Temperature Factors and Dynamics, Coordinated Waters, and Base-Pair Propeller Twist Angles Authors: Westhof, E. / Sundaralingam, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kos.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kos.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ko/1kos ftp://data.pdbj.org/pub/pdb/validation_reports/ko/1kos | 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: 5395.255 Da / Num. of mol.: 1 / Fragment: TPSIC DOMAIN OF TRNA / Mutation: +C49C / Source method: obtained synthetically Details: SEQUENCE FROM YEAST (SACCHAROMYCES CEREVISIAE) TRNA PHE |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: EXPERIMENTS IN 100% D2O CONDUCTED AT 283, 288,293, AND 298 KELVIN; EXPERIMENTS IN 6% D2O/ 94% H2O CONDUCTED AT 274 AND 283 KELVIN. |
-Sample preparation
Details | Contents: 100% D2O, 94% WATER/6% D2O |
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Sample conditions | pH: 6.0 / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker DRX500 / Manufacturer: Bruker / Model: DRX500 / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY STRUCTURES / Conformers calculated total number: 50 / Conformers submitted total number: 8 |