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- PDB-1n1k: NMR Structure for d(CCGCGG)2 -

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Basic information

Entry
Database: PDB / ID: 1n1k
TitleNMR Structure for d(CCGCGG)2
Components5'-D(P*CP*CP*GP*CP*GP*G)-3'
KeywordsDNA / recombination-like / CCGCGG
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / simulated annealing for DNA
AuthorsMonleon, D. / Celda, B.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: NMR study of hexanucleotide d(CCGCGG)(2) containing two triplet repeats of fragile X syndrome.
Authors: Monleon, D. / Esteve, V. / Celda, B.
History
DepositionOct 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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 1.4May 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(P*CP*CP*GP*CP*GP*G)-3'
B: 5'-D(P*CP*CP*GP*CP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
2422D NOESY
2522D TOCSY
262DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM NaCl, NaN3 1%D2O
22000 mM NaCl, NaN3 1%D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM 6.51 atm298 K
22000 mM 6.51 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY4001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.6Molecular Simulations, Inc.refinement
VNMR3.1Varianprocessing
RefinementMethod: simulated annealing for DNA / 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: 10

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