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Basic information

Entry
Database: PDB / ID: 1noq
Titlee-motif structure
Components5'-D(*CP*CP*GP*CP*CP*G)-3'
KeywordsDNA / e-Motif / (ccg)2 DNA duplex
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / distance geometry, restraint molecular dynamics
AuthorsZheng, M. / Huang, X. / Smith, G.K. / Yang, X. / Gao, X.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: Genetically unstable CXG repeats are structurally dynamic and have a high propensity for folding. An NMR and UV spectroscopic study.
Authors: Zheng, M. / Huang, X. / Smith, G.K. / Yang, X. / Gao, X.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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(*CP*CP*GP*CP*CP*G)-3'
B: 5'-D(*CP*CP*GP*CP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)3,5402
Polymers3,5402
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)6 / 6all calculated structures submitted
RepresentativeModel #4closest to the average

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Components

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


Mass: 1770.181 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: this sequence is found in CCG and/or CGG triplet repeat expansion in the 5'-untranslated region of FMR1 gene of fragile X syndrome.

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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
141COSY35
1511H-31P COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

DetailsContents: 2 mM 5'-d(CCGCCG), 0.1 M NaCl, 10 mM Sodium Phosphate, 0.1 mM EDTA
Solvent system: 90 % H20, 10 % D2O
Sample conditionspH: 6.3 / Pressure: ambient / Temperature: 278 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 spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR940101Brukerprocessing
Felix95Accelrysprocessing
X-PLOR3.01Brungerstructure solution
MARDIGRAS3Borgias B.A.refinement
RefinementMethod: distance geometry, restraint molecular dynamics / Software ordinal: 1
Details: the structures are determined with a total of 442 restraints: 430 are NOE-derived distance constraints based on ISPA (isolated spin pair approximation) and 12 are dihedral angle restraints ...Details: the structures are determined with a total of 442 restraints: 430 are NOE-derived distance constraints based on ISPA (isolated spin pair approximation) and 12 are dihedral angle restraints from the analyses of the COSY type of spectra.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 6 / Conformers submitted total number: 6

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