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- PDB-2krp: Solution structure of the E. coli tRNA-Arg2(acg) anticodon stem a... -

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Basic information

Entry
Database: PDB / ID: 2krp
TitleSolution structure of the E. coli tRNA-Arg2(acg) anticodon stem and loop
ComponentsRNA (5'-R(*CP*UP*CP*GP*GP*CP*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')
KeywordsRNA / ASL / modification / arginine / tRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsBilbille, Y. / Agris, P.F.
CitationJournal: To be Published
Title: Solution structure of the tRNA-Arg2 ASL containing the ACG anticodon
Authors: Bilbille, Y. / Cantara, W.A. / Kim, J. / Agris, P.F.
History
DepositionDec 22, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,4411
Polymers5,4411
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 5441.317 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Residues 27-43 of the tRNA ARG 2 containing the ACG anticodon.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D DQF-COSY
1212D 1H-1H NOESY
1322D 1H-1H NOESY
1412D 1H-1H COSY
1522D 1H-13C HSQC
1612D 1H-1H TOCSY
1722D 31P-1H HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM RNA (5'-R(*CP*UP*CP*GP*GP*CP*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1, 90% H2O/10% D2O90% H2O/10% D2O
21 mM RNA (5'-R(*CP*UP*CP*GP*GP*CP*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMRNA (5'-R(*CP*UP*CP*GP*GP*CP*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-11
1 mMRNA (5'-R(*CP*UP*CP*GP*GP*CP*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-22
Sample conditionsIonic strength: 20 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddarddata analysis
SparkyGoddardpeak picking
MOLMOL2.6Koradi, Billeter and Wuthrichdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
VnmrJVariancollection
TopSpinBruker Biospincollection
XwinNMRBruker Biospincollection
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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