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- PDB-2tpk: AN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GE... -

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Basic information

Entry
Database: PDB / ID: 2tpk
TitleAN INVESTIGATION OF THE STRUCTURE OF THE PSEUDOKNOT WITHIN THE GENE 32 MESSENGER RNA OF BACTERIOPHAGE T2 USING HETERONUCLEAR NMR METHODS
ComponentsRNA (MRNA PSEUDOKNOT)
KeywordsRNA / PSEUDOKNOT / T2 / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / DISTANCE GEOMETRY-SIMULATED ANNEALING, ENERGY MINIZATION PROTOCOLS
AuthorsHolland, J.A. / Hansen, M.R. / Du, Z. / Hoffman, D.W.
Citation
Journal: Rna / Year: 1999
Title: An examination of coaxial stacking of helical stems in a pseudoknot motif: the gene 32 messenger RNA pseudoknot of bacteriophage T2.
Authors: Holland, J.A. / Hansen, M.R. / Du, Z. / Hoffman, D.W.
#1: Journal: Nucleic Acids Res. / Year: 1997
Title: An NMR and Mutational Study of the Pseudoknot within the Gene 32 Mrna of Bacteriophage T2: Insights Into a Family of Structurally Related RNA Pseudoknots
Authors: Du, Z. / Hoffman, D.W.
History
DepositionOct 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 1.4Dec 27, 2023Group: 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 (MRNA PSEUDOKNOT)


Theoretical massNumber of molelcules
Total (without water)11,5101
Polymers11,5101
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)1 / 19
Representative

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Components

#1: RNA chain RNA (MRNA PSEUDOKNOT)


Mass: 11509.891 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA WAS CHEMICALLY SYNTHESIZED FROM GENE 32 OF BACTERIOPHAGE T2.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQFCOSY
131TOCSY
141NOESY-TOCSY
151CT-HSQC
161(H)CCH-COSY
171NOESY-HMQC
181HMQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING NMR SPECTROSCOPY ON 13C,15N-LABELED AND SELECTIVELY DEUTERATED T2 PSEUDOKNOT SAMPLE

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerManufacturer: Varian / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
Felixstructure solution
XPLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY-SIMULATED ANNEALING, ENERGY MINIZATION PROTOCOLS
Software ordinal: 1
Details: REFINEMNET DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformers calculated total number: 19 / Conformers submitted total number: 1

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