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- PDB-6aau: Solution Structure for m62A helix 45 in 3' end of 12S rRNA -

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Basic information

Entry
Database: PDB / ID: 6aau
TitleSolution Structure for m62A helix 45 in 3' end of 12S rRNA
ComponentsRNA (24-mer)
KeywordsRNA / stem-loop / h45
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, X. / Wu, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31330018 China
Chinese Academy of SciencesXDPB10, XDB08010101 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function.
Authors: Liu, X. / Shen, S. / Wu, P. / Li, F. / Liu, X. / Wang, C. / Gong, Q. / Wu, J. / Yao, X. / Zhang, H. / Shi, Y.
History
DepositionJul 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value
Revision 1.3Feb 12, 2025Group: Derived calculations / Structure summary
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entry_details
Item: _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening ..._ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (24-mer)


Theoretical massNumber of molelcules
Total (without water)7,7911
Polymers7,7911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1050 Å2
ΔGint6 kcal/mol
Surface area4490 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 RNA (24-mer) / m62A-h45


Mass: 7790.736 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY
121isotropic12D DQF-COSY

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Sample preparation

DetailsType: solution / Contents: 1 mM m62A-h45, 90% H2O/10% D2O / Label: unlabeled_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: m62A-h45 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 2 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
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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