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- PDB-2meq: Structure of Helix 69 from Escherichia coli 23S Ribosomal RNA -

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Basic information

Entry
Database: PDB / ID: 2meq
TitleStructure of Helix 69 from Escherichia coli 23S Ribosomal RNA
ComponentsRNA_(5'-R(P*GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3')
KeywordsRNA / Helix 69 / Ribosomal
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model1
AuthorsJiang, J. / Aduri, R. / Chow, C.S. / Santalucia, J.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.
Authors: Jiang, J. / Aduri, R. / Chow, C.S. / Santalucia, J.
History
DepositionSep 26, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA_(5'-R(P*GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0781
Polymers6,0781
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 / 100CONVERGED LOWEST ENERGY STRUCTURES
RepresentativeModel #1lowest energy

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Components

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


Mass: 6077.673 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-13C NATURAL ABUNDANCE HMQC
1212D 1H-1H NOESY
1312D DQF-COSY
1413D 1H-1H-1H TOCSY-NOESY
1512D 1H-31P HETCOR
1611D 31P
1722D 1H-1H NOESY
1832D 1H-13C HSQC
1933D 1H-13C-1H (H)CCH-COSY
11033D 1H-13C-1H (H)CCH-TOCSY
11133D 1H-13C-13C (H)CCH-TOCSY
11233D 1H-1H-13C NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM RNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 100% D2O100% D2O
21.0 mM RNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-100% 13C; U-100% 15N] RNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3'), 10 mM Potassium Phosphate, 50 mM Potassium Chloride, 0.1 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMRNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3')-11
10 mMPotassium Phosphate-21
50 mMPotassium Chloride-31
0.1 mMEDTA-41
1.0 mMRNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3')-52
10 mMPotassium Phosphate-62
50 mMPotassium Chloride-72
0.1 mMEDTA-82
1.0 mMRNA (5'-P(GP*GP*CP*CP*GP*UP*AP*AP*CP*UP*AP*UP*AP*AP*CP*GP*GP*UP*C)-3')-9[U-100% 13C; U-100% 15N]3
10 mMPotassium Phosphate-103
50 mMPotassium Chloride-113
0.1 mMEDTA-123
Sample conditionsIonic strength: 70 / pH: 7.3 / Pressure: ambient / Temperature: 298.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Varian MercuryVarianMercury4002

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: CONVERGED LOWEST ENERGY STRUCTURES
Conformers calculated total number: 100 / Conformers submitted total number: 10

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