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- PDB-1kos: SOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM ... -

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Entry
Database: PDB / ID: 1kos
TitleSOLUTION NMR STRUCTURE OF AN ANALOG OF THE YEAST TRNA PHE T STEM LOOP CONTAINING RIBOTHYMIDINE AT ITS NATURALLY OCCURRING POSITION
Components5'-R(*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*(CH)P*CP*AP*CP*AP*G)- 3'
KeywordsRNA / TRNA / T STEM LOOP / TRNA DOMAIN / RNA HAIRPIN / RNA FOLDING
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsKoshlap, 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
DepositionMay 3, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*(CH)P*CP*AP*CP*AP*G)- 3'


Theoretical massNumber of molelcules
Total (without water)5,3951
Polymers5,3951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 50LOWEST ENERGY STRUCTURES
Representative

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Components

#1: RNA chain 5'-R(*CP*UP*GP*UP*GP*(5MU)P*UP*CP*GP*AP*UP*(CH)P*CP*AP*CP*AP*G)- 3'


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
141HSQC
151HETCOR
161HETEROTOCSY
171HETEROTOCSY-NOESY
181DQ
NMR detailsText: EXPERIMENTS IN 100% D2O CONDUCTED AT 283, 288,293, AND 298 KELVIN; EXPERIMENTS IN 6% D2O/ 94% H2O CONDUCTED AT 274 AND 283 KELVIN.

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Sample preparation

DetailsContents: 100% D2O, 94% WATER/6% D2O
Sample conditionspH: 6 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX500 / Manufacturer: Bruker / Model: DRX500 / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY STRUCTURES / Conformers calculated total number: 50 / Conformers submitted total number: 8

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