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- PDB-1fzx: NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG -

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Basic information

Entry
Database: PDB / ID: 1fzx
TitleNMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG
Components
  • 5'-D(*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*G)-3'
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / matrix relaxation, simulated annealing with residual dipolar couplings
AuthorsMacDonald, D. / Herbert, K. / Zhang, X. / Pologruto, T. / Lu, P.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Solution structure of an A-tract DNA bend.
Authors: MacDonald, D. / Herbert, K. / Zhang, X. / Pologruto, T. / Lu, P.
History
DepositionOct 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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*GP*CP*AP*AP*AP*AP*AP*AP*CP*GP*G)-3'
B: 5'-D(*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
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 / 20structures with the lowest energy
RepresentativeModel #1

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Components

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


Mass: 3729.470 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*GP*TP*TP*TP*TP*TP*TP*GP*CP*C)-3'


Mass: 3595.338 Da / Num. of mol.: 1 / 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
121DQF-COSY
132HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage)
143HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage)
154HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage)
165HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage)
NMR detailsText: This structure was determined using 13C-H and 15N-H residual dipolar couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 1-12; U-13C/15N20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0
23mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) unlabeled sample20mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0
31.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 13-24; U-13C/15N20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0
41.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 7-12; U-13C/15N20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0
51.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 19-24; U-13C/15N20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0
Sample conditionsIonic strength: 150 KCl / pH: 7 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
MARDIGRAS3.2Jamesiterative matrix relaxation
CORMA5.2Jamesiterative matrix relaxation
X-PLORwith residual dipolar patchBrunger, Tjandrarefinement
RefinementMethod: matrix relaxation, simulated annealing with residual dipolar couplings
Software ordinal: 1
Details: The structure is based on a total of 434 restraints, 220 NOE derived, 90 dihedral angle, 30 Watson-Crick, and 94 residual dipolar coupling restraints
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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