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- PDB-1np5: (GAC)3 parallel duplex -

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Basic information

Entry
Database: PDB / ID: 1np5
Title(GAC)3 parallel duplex
Components5'-D(*GP*AP*CP*GP*AP*CP*GP*AP*C)-3'
KeywordsDNA / DNA trinucleotide repeat / parallel duplex / homo-basepair mismatch / NMR solution structure
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / distance geometry, restraint molecular dynamics
Model type detailsminimized average
AuthorsZheng, M. / Han, X. / Gao, X.
CitationJournal: To be Published
Title: Strand polarity of trinucleotide repeat sequences: NMR studies of parallel/anti-pararell duplex,{d(GAC)3}2
Authors: Zheng, M. / Han, X. / Gao, X.
History
DepositionJan 17, 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(*GP*AP*CP*GP*AP*CP*GP*AP*C)-3'
B: 5'-D(*GP*AP*CP*GP*AP*CP*GP*AP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,5002
Polymers5,5002
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)1 / 10structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

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


Mass: 2749.826 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is found in triplet repeat expansion involving neurogenetic diseases.

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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
141COSY-35
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(GACGACGAC), 0.1 M NaCl, 10 mM Sodium Phosphate, 0.1 mM EDTA
Solvent system: 90 % H20, 10 % D2O
Sample conditionspH: 4.7 / Pressure: ambient / Temperature: 273 K

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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
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 10 / Conformers submitted total number: 1

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