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- PDB-2kzl: Specifier domain and GA motif region of B. subtilis tyrS T box le... -

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Basic information

Entry
Database: PDB / ID: 2kzl
TitleSpecifier domain and GA motif region of B. subtilis tyrS T box leader RNA
ComponentsRNA (55-MER)
KeywordsRNA / Specifier Domain / loop E motif / GA motif / Kink turn / K-turn / T box riboswitch
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsWang, J.
CitationJournal: To be Published
Title: Specifier domain and GA motif region of B. subtilis tyrS T box leader RNA
Authors: Wang, J. / Nikonowicz, E.
History
DepositionJun 18, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (55-MER)


Theoretical massNumber of molelcules
Total (without water)17,7441
Polymers17,7441
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)8 / 50structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: RNA chain RNA (55-MER)


Mass: 17743.633 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Specifier Domain and GA motif region of B. subtilis tyrS T box leader RNA
Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1213D (H)CCH-TOCSY
1312D 1H-1H NOESY
1413D 1H-13C NOESY
2522D 1H-15N HSQC
2623D 1H-15N NOESY
1732D 1H-13C HSQC
1813D (H)CCH-COSY
1913D HCN
21022D 1H-1H NOESY
11112D 1H-15N HSQC
11212D 1H-13C ct-spin-echo difference

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Specifier Domain and GA motif region of B. subtilis tyrS T box leader RNA, 100% D2O100% D2O
21 mM [U-100% 13C; U-100% 15N] Specifier Domain and GA motif region of B. subtilis tyrS T box leader RNA, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 13C; U-100% 15N] Specifier Domain and GA motif region of B. subtilis tyrS T box leader RNA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSpecifier Domain and GA motif region of B. subtilis tyrS T box leader RNA-1[U-100% 13C; U-100% 15N]1
1 mMSpecifier Domain and GA motif region of B. subtilis tyrS T box leader RNA-2[U-100% 13C; U-100% 15N]2
1 mMSpecifier Domain and GA motif region of B. subtilis tyrS T box leader RNA-3[U-100% 13C; U-100% 15N]3
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.8ambient 301 K
26.8288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR softwareName: VnmrJ / Developer: Varian / Classification: collection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 8

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