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- PDB-1cqo: NMR STRUCTURE OF THE PALINDROMIC DNA DECAMER D(GCGTTAACGC)2 -

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Basic information

Entry
Database: PDB / ID: 1cqo
TitleNMR STRUCTURE OF THE PALINDROMIC DNA DECAMER D(GCGTTAACGC)2
Components5'-d(*GP*CP*GP*TP*TP*AP*AP*CP*GP*C)-3'
KeywordsDNA / DOUBLE HELIX / B-DNA / RESTRICTION SITE / HPA 1
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / Restrained molecular dynamics. Relaxation matrix refinement.
AuthorsSmith, J.A. / Tsui, V.T. / Chazin, W.J. / Case, D.A.
CitationJournal: To be Published
Title: NMR Structure of the Palindromic DNA Decamer d(GCGTTAACGC)2
Authors: Smith, J.A. / Tsui, V.T. / Chazin, W.J. / Case, D.A.
History
DepositionAug 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 1.4May 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*CP*GP*TP*TP*AP*AP*CP*GP*C)-3'
B: 5'-d(*GP*CP*GP*TP*TP*AP*AP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0902
Polymers6,0902
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 / 10all calculated structures submitted
RepresentativeModel #5closest to the average

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Components

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


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence is the Hpa1 restriction site.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111Double-Quantum
121DQF-COSY
131E-COSY
1412D NOESY
1522D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM d(GCGTTAACGC); 20mM Na3PO4, 50mM NaCl, 0.1% NaN3.99.9% D2O
22mM d(GCGTTAACGC); 20mM Na3PO4, 50mM NaCl, 0.1% NaN3.95% H2O/5% D2O
Sample conditionsIonic strength: 50mM NaCl, 20mM NaPO4 / pH: 7 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix95Molecular Simulations, Inc.processing
NAB2.1Macke, et. al.structure solution
Amber5Pearlman, et. al.refinement
Amber5Pearlman, et. al.iterative matrix relaxation
RefinementMethod: Restrained molecular dynamics. Relaxation matrix refinement.
Software ordinal: 1
Details: Direct relaxation matrix refinement with explicit solvent. Details in primary citation.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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