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- PDB-2kpr: Monomeric intronic human chl1 gene quadruplex DNA NMR, 17 structures -

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Entry
Database: PDB / ID: 2kpr
TitleMonomeric intronic human chl1 gene quadruplex DNA NMR, 17 structures
Components5'-D(*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3'
KeywordsDNA / G-TETRAD / G-INTERCALATION / V-SHAPED LOOP / DOUBLE-CHAIN REVERSAL LOOP
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKuryavyi, V. / Patel, D.J.
CitationJournal: Structure / Year: 2010
Title: Solution Structure of a Unique G-Quadruplex Scaffold Adopted by a Guanosine-Rich Human Intronic Sequence.
Authors: Kuryavyi, V. / Patel, D.J.
History
DepositionOct 19, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 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(*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3'


Theoretical massNumber of molelcules
Total (without water)6,1031
Polymers6,1031
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)17 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3'


Mass: 6102.917 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: MONOMERIC INTRONIC HUMAN CHL1 GENE QUADRUPLEX DNA NMR, 17 STRUCTURES
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-1H NOESY
1211H-1H TOCSY
1311H- 31P COSY
1411H-1H COSY
1511H-15N JRHMQC
1611H-15N HMBC

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Sample preparation

DetailsContents: 0.5-5.0 mM DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM
Component: DNA (5'-D(*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*GP*TP*GP*GP*GP*T)-3')-1
Conc. range: 0.5-5.0
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6Variancollection
Felix2000Accelrys Software Inc.data analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 17

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