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- PDB-2jrg: NMR solution structure of the anticodon of E. coli TRNA-VAL3 with... -

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Basic information

Entry
Database: PDB / ID: 2jrg
TitleNMR solution structure of the anticodon of E. coli TRNA-VAL3 with 2 modifications (cmo5U34 M6A37)
Components5'-R(*CP*CP*UP*CP*CP*CP*UP*(CM0)P*AP*CP*(6MZ)P*AP*GP*GP*AP*GP*G)-3'
KeywordsRNA / E.coli / Valine / TRNA / ANTICODON STEM LOOP / TRNA DOMAIN / RNA HAIRPIN / URIDINE 5-OXYACETIC ACID / CMO5U / N6-methyladenosine / M6A
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsVendeix, F.A. / Dziergowska, A. / Gustilo, E.M. / Graham, W.D. / Sproat, B. / Malkiewicz, A. / Agris, P.F.
CitationJournal: Biochemistry / Year: 2008
Title: Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding.
Authors: Vendeix, F.A. / Dziergowska, A. / Gustilo, E.M. / Graham, W.D. / Sproat, B. / Malkiewicz, A. / Agris, P.F.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2012Group: Structure summary
Revision 2.0Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.deposit_site / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*CP*CP*UP*CP*CP*CP*UP*(CM0)P*AP*CP*(6MZ)P*AP*GP*GP*AP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)5,4901
Polymers5,4901
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 / 60structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain 5'-R(*CP*CP*UP*CP*CP*CP*UP*(CM0)P*AP*CP*(6MZ)P*AP*GP*GP*AP*GP*G)-3'


Mass: 5490.341 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
1122D 1H-1H COSY
1222D DQF-COSY
1322D 1H-1H TOCSY
1422D 1H-13C HSQC
1522D 1H-1H NOESY
2612D 1H-1H NOESY
1722D 1H-31P HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5-2 mM RNA 17mer, 90% H2O/10% D2O90% H2O/10% D2O
21.5-2 mM RNA 17mer, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.5 mMRNA 17mer1
1.5 mMRNA 17mer2
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.2ambient 295 K
26.2ambient 275 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
VNMRVariancollection
NMRDraw3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: anneal.inp protocol in CNS
NMR constraintsNOE constraints total: 604 / Hydrogen bond constraints total count: 28
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 11 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å

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