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- PDB-1ngu: NMR Structure of Putative 3'Terminator for B. Anthracis pagA Gene... -

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Basic information

Entry
Database: PDB / ID: 1ngu
TitleNMR Structure of Putative 3'Terminator for B. Anthracis pagA Gene Noncoding Strand
Components5'-D(*CP*TP*CP*TP*CP*CP*TP*TP*GP*TP*AP*TP*TP*TP*CP*TP*TP*AP*CP*AP*AP*AP*AP*AP*GP*AP*G)-3'
KeywordsDNA / B-Form DNA Hairpin
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / minimization molecular dynamics
Model type detailsminimized average
AuthorsShiflett, P.R. / Taylor-McCabe, K.J. / Michalczyk, R. / Silks, L.A. / Gupta, G.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Studies on the Hairpins at the 3' Untranslated Region of an Anthrax Toxin Gene
Authors: Shiflett, P.R. / Taylor-McCabe, K.J. / Michalczyk, R. / Silks, L.A. / Gupta, G.
History
DepositionDec 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4May 22, 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: 5'-D(*CP*TP*CP*TP*CP*CP*TP*TP*GP*TP*AP*TP*TP*TP*CP*TP*TP*AP*CP*AP*AP*AP*AP*AP*GP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)8,2251
Polymers8,2251
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)5 / 100Submitted conformers include minimized average from molecular dynamics and 4 representative diverging structures.
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain 5'-D(*CP*TP*CP*TP*CP*CP*TP*TP*GP*TP*AP*TP*TP*TP*CP*TP*TP*AP*CP*AP*AP*AP*AP*AP*GP*AP*G)-3'


Mass: 8225.333 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs on the noncoding strand of the 3' UTR of the pagA (110) gene of Bacillus anthracis.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
142DQF-COSY
NMR detailsText: The structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM 110NC DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl;90% H2O/10% D2O
22mM 110NC DNA; 10mM phosphate buffer pH 6.5; 150mM NaCl;100% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix98Biosymdata analysis
Amber4.1Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A.structure solution
Amber4.1Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A.refinement
RefinementMethod: minimization molecular dynamics / Software ordinal: 1
Details: Structure is derived from 206 NOEs of which, 23 NOEs involvE exchangeable protons in the stem, 131 NOEs involve non-exchangeable protons in the stem, 52 NOEs involve non-exchangeable protons ...Details: Structure is derived from 206 NOEs of which, 23 NOEs involvE exchangeable protons in the stem, 131 NOEs involve non-exchangeable protons in the stem, 52 NOEs involve non-exchangeable protons in the loop, 46 Distance restraints involve hydrogen bonds, and 44 dihedral angle restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: Submitted conformers include minimized average from molecular dynamics and 4 representative diverging structures.
Conformers calculated total number: 100 / Conformers submitted total number: 5

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