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- PDB-2krw: Solution structure of the E coli tRNA-Arg1 (ACG) containing the 2... -

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Basic information

Entry
Database: PDB / ID: 2krw
TitleSolution structure of the E coli tRNA-Arg1 (ACG) containing the 2-thiocytidine modification in position 32
ComponentsRNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')
KeywordsRNA / tRNA / 2-thiocytidine / ASL / modification
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsBilbille, Y. / Agris, P.F.
CitationJournal: To be Published
Title: Solution structure of the tRNA-Arg1 (ACG) containing the 2-thiocytidine modification in position 32
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 2.0May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _chem_comp.mon_nstd_flag / _database_2.pdbx_DOI ..._chem_comp.mon_nstd_flag / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,4571
Polymers5,4571
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)11 / 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*(N)P*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')


Mass: 5457.382 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1322D DQF-COSY
1412D 1H-1H COSY
1512D 1H-1H TOCSY
1622D 1H-13C HSQC
1722D 1H-31P HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-1, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM RNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.7 mMRNA (5'-R(*CP*UP*CP*GP*GP*(N)P*UP*AP*CP*GP*AP*AP*CP*CP*GP*AP*G)-3')-11
0.7 mMRNA (5'-R(*CP*UP*CP*GP*GP*(N)P*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 AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
TopSpinBruker Biospincollection
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
MOLMOLKoradi, Billeter and Wuthrichdata analysis
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: 11

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