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- PDB-2g1w: NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1 -

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Basic information

Entry
Database: PDB / ID: 2g1w
TitleNMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1
Components5'-R(*GP*GP*GP*GP*UP*GP*GP*CP*UP*CP*CP*CP*CP*UP*AP*AP*CP*AP*GP*CP*CP*G)-3'
KeywordsRNA / tmRNA / PK1 / pseudoknot / trans-translation
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / CNS dynamical annealing protocol for nucleic acids
AuthorsNonin-Lecomte, S. / Dardel, F.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation.
Authors: Nonin-Lecomte, S. / Felden, B. / Dardel, F.
History
DepositionFeb 15, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 29, 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'-R(*GP*GP*GP*GP*UP*GP*GP*CP*UP*CP*CP*CP*CP*UP*AP*AP*CP*AP*GP*CP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)7,0641
Polymers7,0641
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)15 / 100structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*GP*GP*GP*GP*UP*GP*GP*CP*UP*CP*CP*CP*CP*UP*AP*AP*CP*AP*GP*CP*CP*G)-3'


Mass: 7064.258 Da / Num. of mol.: 1 / Mutation: C1G, G13C / Source method: obtained synthetically
Details: The sequence of this RNA naturally exists in Aquifex aeolicus (Bacteria)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
221HCN, 1H 13C HSQC, 1H 13C constant time HSQC, 1H 13C long-range HSQC, (H)CCH-TOCSY, (H)CCH E.COSY, HCC-TOCSY-CCH-E.COSY, 3D NOESY-HSQC
131HMBC, 1H 15N TROSY, 2JNN HNN-COSY, 2JNH HNN-COSY, 3D NOESY-HMBC
2422D NOESY, TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM 13C,15N PK1, 50mM NaCl, 0.5 mM EDTA95%H2O-5%D2O and 100% D2O
21mM unlabeled PK1, 50mM NaCl, 0.5 mM EDTA95%H2O-5%D2O and 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 6.3ambient 278 K
250mM NaCl 6.3ambient 293 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
NameVersionDeveloperClassification
UXNMR3.1Brukercollection
Felix2000.1MSI Inc.data analysis
CNS1.1Brunger, Adams,Clore, DeLano,Gross, Grosse-Kunstleve, Jiang, Kuzewski, Nilges, Pannu, Read, Rice, Simmonson, Warrenrefinement
MOLMOL2K.1Reto Koradidata analysis
RefinementMethod: CNS dynamical annealing protocol for nucleic acids / Software ordinal: 1
Details: A- dynamical annealing protocol: 1. TAMD 30 ps at 20000K 2. first cooling stage TAMD 40ps 3. second slow cooling annealing stage, restrained molecular dynamics 35ps. 4. 10 cycles of energy ...Details: A- dynamical annealing protocol: 1. TAMD 30 ps at 20000K 2. first cooling stage TAMD 40ps 3. second slow cooling annealing stage, restrained molecular dynamics 35ps. 4. 10 cycles of energy minimization of 300 steps each. B- Energy minimization: 1-TAMD 10ps at 300K, 2- cooling over 9 ps and 10 Powell cycles of 800 steps each.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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