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- PDB-1mv6: The tandem, Sheared PP Pairs in 5'(rGGCPPGCCU)2 -

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Basic information

Entry
Database: PDB / ID: 1mv6
TitleThe tandem, Sheared PP Pairs in 5'(rGGCPPGCCU)2
Components5'-R(*GP*GP*CP*(P5P)P*(P5P)P*GP*CP*CP*U)-3'
KeywordsRNA / ribonucleic acid / duplex / tandem mismatch / purine
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsZnosko, B.M. / Burkard, M.E. / Krugh, T.R. / Turner, D.H.
Citation
Journal: Biochemistry / Year: 2002
Title: Molecular Recognition in Purine-Rich Internal Loops: Thermodynamic, Structural, and Dynamic Consequences of Purine for Adenine Substitutions in 5'(rGGCAAGCCU)2
Authors: Znosko, B.M. / Burkard, M.E. / Krugh, T.R. / Turner, D.H.
#1: Journal: Biochemistry / Year: 2002
Title: Sheared Aanti-Aanti Base Pairs in a Destabilizing 2x2 Internal Loop: The NMR Structure of 5'(rGGCAAGCCU)2
Authors: Znosko, B.M. / Burkard, M.E. / Schroeder, S.J. / Krugh, T.R. / Turner, D.H.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_struct_assembly / pdbx_struct_oper_list / struct_conn
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
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'-R(*GP*GP*CP*(P5P)P*(P5P)P*GP*CP*CP*U)-3'
B: 5'-R(*GP*GP*CP*(P5P)P*(P5P)P*GP*CP*CP*U)-3'


Theoretical massNumber of molelcules
Total (without water)5,6822
Polymers5,6822
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)3 / 33Random Structures to show variety
RepresentativeModel #3closest to the average

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Components

#1: RNA chain 5'-R(*GP*GP*CP*(P5P)P*(P5P)P*GP*CP*CP*U)-3'


Mass: 2840.755 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 90% H2O, 10% D2O90% H2O/10% D2O
22mM RNA, 80 mM NaCl, 10mM phosphate buffer, 0.5mM EDTA; 99.996% D2O99.996% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
190% H2O, 10% D2O 6.5ambient 273 K
299.996% D2O 7.7ambient 303 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: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.2Variancollection
Felix2000MSIdata analysis
Discover95MSIstructure solution
Discover95MSIrefinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
Details: total of 63 interproton distance restraints per strand, 18 hydrogen bond restraints, and 50 dihedral angle restraints per strand.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: Random Structures to show variety
Conformers calculated total number: 33 / Conformers submitted total number: 3

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