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- PDB-1c2q: SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOME... -

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Basic information

Entry
Database: PDB / ID: 1c2q
TitleSOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS
Components
  • 5'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3'
  • 5'-R(GAGCACCAU)-3'
KeywordsDNA-RNA HYBRID / DNA/RNA HYBRID / ALPHAT-ANOMERIC THYMIDINE / 3'-3'/5'-5' PHOSPHODIESTER LINKAGES
Function / homologyDNA / RNA
Function and homology information
MethodSOLUTION NMR / SIMULATED ANNEALING, MOLECULAR DYNAMICS
Model type detailsminimized average
AuthorsGermann, M.W. / Aramini, J.M.
Citation
Journal: Biochemistry / Year: 1999
Title: Solution structure of a DNA.RNA hybrid containing an alpha-anomeric thymidine and polarity reversals: d(ATGG-3'-3'-alphaT-5'-5'-GCTC). r(gagcaccau).
Authors: Aramini, J.M. / Germann, M.W.
#1: Journal: Nucleic Acids Res. / Year: 1998
Title: NMR solution structures of [d(GCGAAT-3'-3'-(alpha-T)-5'-5'-CGC)2] and its unmodified control
Authors: Aramini, J.M. / Mujeeb, A. / Germann, M.W.
History
DepositionJul 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
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'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3'
B: 5'-R(GAGCACCAU)-3'


Theoretical massNumber of molelcules
Total (without water)5,6022
Polymers5,6022
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: DNA chain 5'-D(ATGG-3'-3'-(T3P)-5'-5'-GCTC)-3'


Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC
#2: RNA chain 5'-R(GAGCACCAU)-3'


Mass: 2854.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
13131P-1H CORRELATION SPECTROSCOPY
2422D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES

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Sample preparation

Details
Solution-IDContents
10.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O
20.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH 6.7, 90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.6AMBIENT 298 K
26.7AMBIENT 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.1BRUKERcollection
MARDIGRAS3.2BORGIAS & JAMES, 1989iterative matrix relaxation
CORMA5.2BORGIAS & JAMES, 1988data analysis
Sparky3.33UCSFdata analysis
Amber4.1PEARLMAN ET AL., 1995refinement
SPHINX/LINSHAWIDMER & WUTHRICH, 1987data analysis
Curves5.1LAVERY & SKLENAR, 1996data analysis
Amber4.1PEARLMAN ET AL., 1995structure solution
RefinementMethod: SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE IS BASED ON A TOTAL OF 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE ...Details: THE STRUCTURE IS BASED ON A TOTAL OF 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS DERIVED FROM PSEUDOROTATION ANALYSIS; 45 RIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS (BROAD, N-TYPE); 46 WATSON-CRICK DISTANCE AND ANGLE RESTRAINTS. THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF RMD/REM STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL STRUCTURE CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM WITHIN AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID PARAMETERIZATION. ALL CALCULATIONS WERE CONDUCTED IN VACUO, USING A DISTANCE DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT-OFF FOR NON-BONDED INTERACTIONS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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