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- PDB-1ecu: SOLUTION STRUCTURE OF E2F BINDING DNA FRAGMENT GCGCGAAAC-T-GTTTCGCGC -

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Basic information

Entry
Database: PDB / ID: 1ecu
TitleSOLUTION STRUCTURE OF E2F BINDING DNA FRAGMENT GCGCGAAAC-T-GTTTCGCGC
ComponentsDNA (5'-D(*GP*CP*GP*CP*GP*AP*AP*AP*CP*TP*GP*TP*TP*TP*CP*GP*CP*GP*C)-3')
KeywordsDNA / double strands / loop
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / Molecular Dynamics with Particle-Particle Particle-Mesh method; Iterative Relaxation Matrix Approach with generalized order parameters
AuthorsWu, J.H. / Chang, C. / Pei, J.M. / Xiao, Q. / Shi, Y.Y.
CitationJournal: to be published / Year: 2000
Title: Solution structure of E2F binding DNA fragment GCGCGAAAC-T-GTTTCGCGC studied by Molecular Dynamics Simulation and Two Dimensional NMR experiment
Authors: Wu, J.H. / Chang, C. / Pei, J.M. / Xiao, Q. / Shi, Y.Y.
History
DepositionJan 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2000Provider: 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: DNA (5'-D(*GP*CP*GP*CP*GP*AP*AP*AP*CP*TP*GP*TP*TP*TP*CP*GP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,8221
Polymers5,8221
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)2 / 2all calculated structures submitted
Representative

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Components

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


Mass: 5821.759 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF E2F BINDING DNA / Source method: obtained synthetically
Details: The sequence is formed by adding CTG loop to ends of ds(GCGCGAAA:TTTCGCGC), which occurs naturally in humans.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
NMR detailsText: Solvent suppression was realized by WATERGATE method.

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Sample preparation

Details
Solution-IDContentsSolvent system
13.5mM DNA fragment; 50mM phosphate buffer, pH 7.0; 150mM NaCl; 1mM EDTA; 1mM NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
2same as 1 except in D2O99.96% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.1Brukercollection
IRMA0.1Alexandre Bonviniterative matrix relaxation
GROMOS96W.F.van Gunsterenrefinement
RefinementMethod: Molecular Dynamics with Particle-Particle Particle-Mesh method; Iterative Relaxation Matrix Approach with generalized order parameters
Software ordinal: 1
Details: Initial structure for model 1 is A-DNA, while that for model 2 is B-DNA. First we applied 640ps free MD with 18 Na+ counterions and 2789 waters for A-DNA and 2303 waters for B-DNA. Then we ...Details: Initial structure for model 1 is A-DNA, while that for model 2 is B-DNA. First we applied 640ps free MD with 18 Na+ counterions and 2789 waters for A-DNA and 2303 waters for B-DNA. Then we applied 4 cycles of IRMA with 174 NOE restraints and 19 hydrogen bond restraints
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 2 / Conformers submitted total number: 2

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