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- PDB-2mg8: Solution structure of TFF1 Estrogen Response Element complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2mg8
TitleSolution structure of TFF1 Estrogen Response Element complexed with DNA Bis-intercalating Anticancer Drug XR5944 (MLN944)
Components
  • 5'-D(*AP*GP*GP*TP*CP*AP*CP*GP*GP*TP*GP*GP*CP*CP*A)-3'
  • 5'-D(*TP*GP*GP*CP*CP*AP*CP*CP*GP*TP*GP*AP*CP*CP*T)-3'
KeywordsDNA / breast cancer drug / DNA bis-intercalation / ERE-targeting small molecule anticancer drug
Function / homologyChem-XR2 / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsfewest violations, model9
AuthorsLin, C.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator.
Authors: Lin, C. / Mathad, R.I. / Zhang, Z. / Sidell, N. / Yang, D.
History
DepositionOct 30, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Other / Structure summary
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*AP*GP*GP*TP*CP*AP*CP*GP*GP*TP*GP*GP*CP*CP*A)-3'
B: 5'-D(*TP*GP*GP*CP*CP*AP*CP*CP*GP*TP*GP*AP*CP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3624
Polymers9,1812
Non-polymers1,1812
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 50structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

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


Mass: 4635.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: strand 1
#2: DNA chain 5'-D(*TP*GP*GP*CP*CP*AP*CP*CP*GP*TP*GP*AP*CP*CP*T)-3'


Mass: 4545.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: strand 2
#3: Chemical ChemComp-XR2 / 1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL)-12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL]PHENAZIN-10-IUM


Mass: 590.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H38N8O2
Nonpolymer detailsUNDER THE EXPERIMENTAL CONDITIONS, LIGAND XR2 IS DEPROTONATED (LACKING ATOMS H10 AND H10').

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 200-300 uM DNA (5'-D(*(X)*(X))-3'), 100% D2O / Solvent system: 100% D2O
SampleUnits: uM / Component: DNA (5'-D(*(X)*(X))-3')-1 / Conc. range: 200-300
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospincollection
SparkyGoddardchemical shift assignment
X-PLORSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 14

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