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- PDB-2kd4: Solution structure and thermodynamics of 2',5' RNA intercalation -

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Basic information

Entry
Database: PDB / ID: 2kd4
TitleSolution structure and thermodynamics of 2',5' RNA intercalation
Components5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'
KeywordsRNA / proflavine / intercalation / 2' / 5' RNA / nearest-neighbor exclusion
Function / homologyPROFLAVIN / RNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHorowitz, E.D. / Lilavivat, S. / Holladay, B.W. / Germann, M.W. / Hud, N.V.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Solution structure and thermodynamics of 2',5' RNA intercalation.
Authors: Horowitz, E.D. / Lilavivat, S. / Holladay, B.W. / Germann, M.W. / Hud, N.V.
History
DepositionJan 2, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_polymer_linkage / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'
B: 5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5324
Polymers5,1132
Non-polymers4182
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain 5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'


Mass: 2556.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic 2',5' RNA
#2: Chemical ChemComp-PRL / PROFLAVIN / Proflavine


Mass: 209.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11N3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY
12131P-1H HETCOR
1311H-1H TOCSY
14131P-decoupled 1H-1H COSY
2511H-1H NOESY with WATERGATE water suppression

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Sample preparation

DetailsContents: 2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4, 99.9% D2O
Solvent system: 99.9% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mM2',5' RNA-11
4 mMPROFLAVINE-21
60 mMSodium phosphate-31
200 mMsodium chloride-41
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1260 6.5 1 atm282 K
2130 1 atm282 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
XwinNMRBruker Biospindata analysis
XwinNMRBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed
NMR constraintsNA alpha-angle constraints total count: 14 / NA other-angle constraints total count: 14 / NOE constraints total: 378 / NOE intraresidue total count: 258 / NOE medium range total count: 378 / NOE sequential total count: 258
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 1

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