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- PDB-5wq1: Solution Structure of the first stem-loop of Escherichia coli DsrA RNA -

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Basic information

Entry
Database: PDB / ID: 5wq1
TitleSolution Structure of the first stem-loop of Escherichia coli DsrA RNA
ComponentsDsrA-SL1
KeywordsRNA / first stem-loop
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsWu, P. / Wu, J. / Shi, Y.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0500700 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08010100 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08030302 China
Chinese National Natural Science Foundation31330018 China
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: The important conformational plasticity of DsrA sRNA for adapting multiple target regulation
Authors: Wu, P. / Liu, X. / Yang, L. / Sun, Y. / Gong, Q. / Wu, J. / Shi, Y.
History
DepositionNov 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.3May 29, 2024Group: 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: DsrA-SL1


Theoretical massNumber of molelcules
Total (without water)7,3171
Polymers7,3171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4760 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 160structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain DsrA-SL1


Mass: 7317.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
123isotropic12D 1H-15N HNN-COSY
133isotropic12D 1H-15N HSQC
143isotropic12D 1H-15N HSQC NH2 only
153isotropic13D 1H-15N NOESY
262isotropic12D 1H-1H NOESY
272isotropic12D DQF-COSY
282isotropic12D 1H-1H TOCSY
294isotropic12D 1H-13C HSQC aliphatic
2114isotropic12D 1H-13C HSQC aromatic
2104isotropic12D HCN
2134isotropic13D (H)CCH-TOCSY
2124isotropic13D (H)CCH-COSY
2144isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM RNA (23-MER), 10 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2ONA_H2O90% H2O/10% D2O
solution20.7 mM RNA (23-MER), 10 mM sodium phosphate, 50 mM sodium chloride, 100% D2ONA_D2O100% D2O
solution30.7 mM [U-13C; U-15N] RNA (23-MER), 10 mM sodium phosphate, 50 mM potassium chloride, 90% H2O/10% D2OCN_H2O90% H2O/10% D2O
solution40.7 mM [U-13C; U-15N] RNA (23-MER), 10 mM sodium phosphate, 50 mM sodium chloride, 100% D2OCN_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMRNA (23-MER)natural abundance1
10 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.7 mMRNA (23-MER)natural abundance2
10 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
0.7 mMRNA (23-MER)[U-13C; U-15N]3
10 mMsodium phosphatenatural abundance3
50 mMpotassium chloridenatural abundance3
0.7 mMRNA (23-MER)[U-13C; U-15N]4
10 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
160 mMH2O6.5 1 atm283 K
260 mMD2O6.5 1 atm303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian INOVAVarianINOVA7002

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
XwinNMRBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 160 / Conformers submitted total number: 20

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