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- PDB-2n6w: NMR Assignment and structure of CssA Thermometer from Neisseria m... -

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Basic information

Entry
Database: PDB / ID: 2n6w
TitleNMR Assignment and structure of CssA Thermometer from Neisseria meningitidis
ComponentsRNA (68-MER)
KeywordsRNA / RNA regulation / pathogen / RNA thermometer / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsBarnwal, R. / Godin, K. / Varani, G. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis.
Authors: Barnwal, R.P. / Loh, E. / Godin, K.S. / Yip, J. / Lavender, H. / Tang, C.M. / Varani, G.
History
DepositionAug 28, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
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 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (68-MER)


Theoretical massNumber of molelcules
Total (without water)21,6551
Polymers21,6551
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 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (68-MER)


Mass: 21654.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Neisseria meningitidis (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H TOCSY
1412D 1H-1H NOESY
1512D DQF-COSY
1613D (H)CCH-TOCSY
1713D 1H-13C NOESY
181ARTSY
191ARTSY

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Sample preparation

DetailsContents: 0.4-1.1 mM CssA RNA thermometer (68-MER), 0.4-1.1 mM 13C/15N-uniformly labeled CssA RNA thermometer (68-MER), 0.4-1.1 mM 13C/15N-AU labeled CssA RNA thermometer (68-MER), 0.4-1.1 mM ...Contents: 0.4-1.1 mM CssA RNA thermometer (68-MER), 0.4-1.1 mM 13C/15N-uniformly labeled CssA RNA thermometer (68-MER), 0.4-1.1 mM 13C/15N-AU labeled CssA RNA thermometer (68-MER), 0.4-1.1 mM partially deuterated CssA RNA thermometer (68-MER), 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCssA RNA thermometer (68-MER)-10.4-1.11
mMCssA RNA thermometer (68-MER)-213C/15N-uniformly labeled0.4-1.11
mMCssA RNA thermometer (68-MER)-313C/15N-AU labeled0.4-1.11
mMCssA RNA thermometer (68-MER)-4partially deuterated0.4-1.11
Sample conditionspH: 6 / Pressure: ambient / Temperature: 280 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Agilent INOVAAgilentINOVA9003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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