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- PDB-5kih: Structural impact of single ribonucleotides in DNA -

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Basic information

Entry
Database: PDB / ID: 5kih
TitleStructural impact of single ribonucleotides in DNA
Components
  • DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3')
  • DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3')
KeywordsDNA / RNA / Ribonucleotides
Function / homologyDNA / DNA/RNA hybrid
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / matrix relaxation, molecular dynamics
AuthorsEvich, M. / Spring-Connell, A.M. / Storici, F. / Germann, M.W.
CitationJournal: Chembiochem / Year: 2016
Title: Structural Impact of Single Ribonucleotide Residues in DNA.
Authors: Evich, M. / Spring-Connell, A.M. / Storici, F. / Germann, M.W.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3')
B: DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)5,4882
Polymers5,4882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area850 Å2
ΔGint-4 kcal/mol
Surface area3610 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 6structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3')


Mass: 2762.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3')


Mass: 2724.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY 250 ms
222isotropic12D NOESY
131isotropic12D Low Flip COSY
141isotropic22D 1H-13C HSQC
151isotropic12D constant time NOESY
1101isotropic12D 1H-31P CORR
191isotropic12D NOESY 150 ms
181isotropic11D 1H
171isotropic11D 31P
262isotropic11D 1H 1-1 jump and return

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate, 100% D2O100% D2O, pH 6.6D2O_sample100% D2O
solution21 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3'), 10 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O90% H2O, 10% D2O, pH 7.0H2O_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3')natural abundance1
1 mMDNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3')natural abundance1
100 %D2O100% deuterium1
100 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
1 mMDNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3')natural abundance2
1 mMDNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3')natural abundance2
10 %D2O100% deuterium2
100 mMsodium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1110 mMD2O_conditions6.6ambient atm294 K
2110 mMH2O_conditions7ambient atm294 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
Sparky3.33Goddardchemical shift assignment
TopSpinBruker Biospincollection
CORMAThomas Jamesrefinement
MARDIGRASThomas Jamesrefinement
RefinementMethod: matrix relaxation, molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 6 / Conformers submitted total number: 2

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