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- PDB-1rrr: RNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 10 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1rrr
TitleRNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 10 STRUCTURES
Components
  • RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3')
  • RNA (5'-R(*GP*CP*UP*UP*CP*UP*CP*UP*UP*C)-3')
KeywordsRNA / RNA DUPLEX / PURINE/PYRIMIDINE-RICH STRANDS / A-FORM
Function / homologyRNA
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsGyi, J.I. / Lane, A.N. / Conn, G.L. / Brown, T.
Citation
Journal: Biochemistry / Year: 1998
Title: Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes.
Authors: Gyi, J.I. / Lane, A.N. / Conn, G.L. / Brown, T.
#1: Journal: Biochemistry / Year: 1996
Title: Comparison of the Thermodynamic Stabilities and Solution Conformations of DNA.RNA Hybrids Containing Purine-Rich and Pyrimidine-Rich Strands with DNA and RNA Duplexes
Authors: Gyi, J.I. / Conn, G.L. / Lane, A.N. / Brown, T.
History
DepositionOct 21, 1997Processing site: BNL
Revision 1.0Apr 22, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_database_status.process_site / _pdbx_nmr_software.name
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: RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3')
B: RNA (5'-R(*GP*CP*UP*UP*CP*UP*CP*UP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,3392
Polymers6,3392
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)10 / 32LOWEST POTENTIAL ENERGY AND MINIMAL VIOLATIONS AND ACCEPTABLE STEREOCHEMISTRY
Representative

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Components

#1: RNA chain RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3') / RR10.RY10


Mass: 3287.076 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(*GP*CP*UP*UP*CP*UP*CP*UP*UP*C)-3') / RR10.RY10


Mass: 3051.804 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY

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Sample preparation

Sample conditionspH: 7.0 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionDeveloperClassification
Discover95MOLECULAR SIMULATIONS INC.refinement
Felix95structure solution
NUCFITstructure solution
pfitstructure solution
DISCOVER 95.0 (INSIGHTII)(INSIGHTII)structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, RIBOSE PSEUDOROTATIONAL PHASE ANGLES AND AMPLITUDES CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST SQUARES/GRID- ...Details: DISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, RIBOSE PSEUDOROTATIONAL PHASE ANGLES AND AMPLITUDES CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST SQUARES/GRID-SEARCH METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). INTERNUCLEOTIDE DISTANCE CONSTRAINTS CALCULATED FROM NOE BUILD-UP CURVES. STRUCTURES CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN AMBER FORCEFIELD AND A DISTANCE DEPENDENT DIELECTRIC CONSTANT.
NMR ensembleConformer selection criteria: LOWEST POTENTIAL ENERGY AND MINIMAL VIOLATIONS AND ACCEPTABLE STEREOCHEMISTRY
Conformers calculated total number: 32 / Conformers submitted total number: 10

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