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- PDB-2au4: Class I GTP aptamer -

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Basic information

Entry
Database: PDB / ID: 2au4
TitleClass I GTP aptamer
ComponentsClass I RNA aptamer to GTP
KeywordsRNA / aptamer
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics
Model type detailsminimized average
AuthorsCarothers, J.M. / Davis, J.H. / Chou, J.J. / Szostak, J.W.
CitationJournal: Rna / Year: 2006
Title: Solution structure of an informationally complex high-affinity RNA aptamer to GTP.
Authors: Carothers, J.M. / Davis, J.H. / Chou, J.J. / Szostak, J.W.
History
DepositionAug 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class I RNA aptamer to GTP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8472
Polymers13,3241
Non-polymers5231
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 / -
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain Class I RNA aptamer to GTP


Mass: 13323.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro selection
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 13C-separated NOESY
1233D 15N-separated NOESY
1332D NOESY
144DQF-COSY
4552D 1H decoupled 13C-1H CT HSQC
4652D 13C-1H CT-TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13.3 mM Class I aptamer U-15N, 13C, 3.63 mM GTP ligand NA, 10 % phosphate buffer NA, 99% D2O99% D2O
20.9 mM Class I aptamer NA, 0.99 nM GTP ligand U-15N, 13C, 10 % phospate buffer NA, 99% D2O99% D2O
33.3 mM Class I aptamer U-15N, 13C; 3.63 mM GTP ligand NA; 10 % phosphate buffer NA, 95% H2O, 5% D2O95% H2O/5% D2O
40.9 mM Class I aptamer NA; 0.99 nM GTP ligand U-15N, 13C; 10 % phospate buffer NA, 95% H2O, 5% D2O95% H2O/5% D2O
50.8 mM Class I RNA aptamer U-15N,13C, 0.9 mM GTP NA, 10% phosphate buffer NA, 95% H2O, 5% D2O95% H2O/5% D2O
60.5 mM Class I RNA aptamer U-15N,13C, 0.55 mM GTP NA, 18 mL/mg Pf1 phage NA, 10% phosphate buffer NA, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15 mM MgCl2, 75 mM KCl 6.1ambient 288 K
25 mM MgCl2, 75 mM KCl 6.1ambient 303 K
35 mM MgCl2, 75 mM KCl 6.1ambient 298 K
45 mM MgCl2, 75 mM KCl 6.8ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002
Varian UNITYVarianUNITY4003
Bruker AVANCEBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglioprocessing
XPLOR-NIH2.9.2Clore, Tjandra, Schwieters, Kuszewskistructure solution
Sparky3Kneller and Kuntzdata analysis
XPLOR-NIH2.9.2Clore, Tjandra, Schwieters, Kuszewskirefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1 / Details: structures are based on a total of 434 restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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