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- PDB-2o4y: Solution structure of a DNA duplex containing the universal base ... -

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Basic information

Entry
Database: PDB / ID: 2o4y
TitleSolution structure of a DNA duplex containing the universal base 5-nitroindole-3-carboxamide
Components
  • DNA (5'-D(*CP*GP*TP*TP*GP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*G)-3')
KeywordsDNA / DNA universal base nitroindole intercalation dynamics
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsGallego, J. / Loakes, D.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide.
Authors: Gallego, J. / Loakes, D.
History
DepositionDec 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Refinement description / Source and taxonomy
Category: diffrn / diffrn_radiation ...diffrn / diffrn_radiation / diffrn_radiation_wavelength / ndb_struct_conf_na / pdbx_entity_src_syn / pdbx_nmr_details / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_representative / pdbx_nmr_sample_details / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_nmr_details.text / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ..._pdbx_nmr_details.text / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_refine.details / _pdbx_nmr_refine.method / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_representative.conformer_id / _pdbx_nmr_representative.selection_criteria / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Remark 400COMPOUND THE STRUCTURE OF ONE SYMMETRICAL HALF OF THE SELF-COMPLEMENTARY (5'-D(*GP*TP*AP*CP*(NCX)P* ...COMPOUND THE STRUCTURE OF ONE SYMMETRICAL HALF OF THE SELF-COMPLEMENTARY (5'-D(*GP*TP*AP*CP*(NCX)P* AP*CP*GP*CP*GP*TP*TP*GP*TP*AP*C)-3')2 DUPLEX IS PROVIDED. THUS IN THE EXPERIMENT, CHAINS A AND B HAD THE SAME SEQUENCE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,9232
Polymers4,9232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1460 Å2
ΔGint3 kcal/mol
Surface area3060 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)28 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (5'-D(*GP*TP*AP*CP*(NCX)P*AP*CP*G)-3')


Mass: 2505.674 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized by solid phase methods using 5-nitroindole-3-carboxamide phosphoramidite
Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*GP*TP*TP*GP*TP*AP*C)-3')


Mass: 2417.603 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-IDType
1112D NOESY
1212D DQF-COSY
1312D TOCSY
1412D 1H-31P HETCOR
2522D ROESY
NMR detailsText: Model 1 is the best representative conformer based on lowest total energy. Model 2 is the best representative conformer based on restraint energy. Models 1 and 2 represent two different ...Text: Model 1 is the best representative conformer based on lowest total energy. Model 2 is the best representative conformer based on restraint energy. Models 1 and 2 represent two different stacking configurations of the nitroindole base.

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.9 mM DNA, 20 mM phosphate buffer, 100 mM NaCl, 0.2 mM EDTA, 100% D2Osample 1100% D2O
solution21.9 mM DNA, 20 mM phosphate buffer, 100 mM NaCl, 0.2 mM EDTA, 90% H2O/10% D2Osample 290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.9 mMDNAnatural abundance1
20 mMphosphate buffernatural abundance1
100 mMNaClnatural abundance1
0.2 mMEDTAnatural abundance1
1.9 mMDNAnatural abundance2
20 mMphosphate buffernatural abundance2
100 mMNaClnatural abundance2
0.2 mMEDTAnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mM NaCl, 20mM sodium phosphate Not definedcondition 16.9 Not definedambient 311 K
2100 mM NaCl, 20mM sodium phosphate Not definedcondition 26.9 Not definedambient 287 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker biospin corporationcollection
NMRPipe2004F. Delaglio, S. Grzesiek, G. Zhu, G.W. Vuister, J. Pfeifer and A. Baxprocessing
Sparky3.11T.D. Goddard and D.G. Knellerdata analysis
Amber8D.A. Case et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 4
Details: The structures were determined using simulated annealing using molecular dynamics with 440 NOE distance restraints (144 intra-residue and 296 inter-residue), 16 hydrogen bonding distance ...Details: The structures were determined using simulated annealing using molecular dynamics with 440 NOE distance restraints (144 intra-residue and 296 inter-residue), 16 hydrogen bonding distance restraints and 167 dihedral restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 28

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