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- PDB-1lej: NMR Structure of a 1:1 Complex of Polyamide (Im-Py-Beta-Im-Beta-I... -

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Entry
Database: PDB / ID: 1lej
TitleNMR Structure of a 1:1 Complex of Polyamide (Im-Py-Beta-Im-Beta-Im-Py-Beta-Dp) with the Tridecamer DNA Duplex 5'-CCAAAGAGAAGCG-3'
Components
  • 5'-D(*CP*CP*AP*AP*AP*GP*AP*GP*AP*AP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*TP*TP*CP*TP*CP*TP*TP*TP*GP*G)-3'
KeywordsDNA / POLYAMIDE / PURINE TRACT / BETA ALANINE / MINOR GROOVE
Function / homologyChem-P11 / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics, simulated annealing, matrix relaxation, NOE-derived distance restraints.
AuthorsUrbach, A.R. / Love, J.J. / Ross, S.A. / Dervan, P.B.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structure of a beta-alanine-linked polyamide bound to a full helical turn of purine tract DNA in the 1:1 motif.
Authors: Urbach, A.R. / Love, J.J. / Ross, S.A. / Dervan, P.B.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 5'-D(*CP*CP*AP*AP*AP*GP*AP*GP*AP*AP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*TP*TP*CP*TP*CP*TP*TP*TP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8583
Polymers7,9432
Non-polymers9151
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 40structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 4018.652 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was designed and synthesized for this study.
#2: DNA chain 5'-D(*CP*GP*CP*TP*TP*CP*TP*CP*TP*TP*TP*GP*G)-3'


Mass: 3924.544 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence was designed and synthesized for this study.
#3: Chemical ChemComp-P11 / IMIDAZOLE-PYRROLE-BETA ALANINE-IMIDAZOLE-BETA ALANINE-IMIDAZOLE-PYRROLE-BETA ALANINE-DIMETHYLAMINO PROPYLAMIDE


Mass: 914.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H56N17O8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 3.67 millimolar polyamide-DNA complex, 10 millimolar sodium phosphate, pH 7.0, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 10 Millimolar / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1 BVarian Associates, Inc.collection
NMRPipe1Delalgio, grzesiek, Vuister, Zhu, Pfeifer, & Baxprocessing
NMRView4.1.2Johnson, & Blevinsdata analysis
MARDIGRAS3.2Borgias, & Jamesiterative matrix relaxation
Amber6Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weinerstructure solution
SANDER MODULE OF AMBER 6.0 PACKAGE (2000)Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weinerrefinement
RefinementMethod: restrained molecular dynamics, simulated annealing, matrix relaxation, NOE-derived distance restraints.
Software ordinal: 1
Details: The structure calculations used 548 distance restraints. 508 were NOE-derived, and 40 were for Watson-Crick hydrogen bonds.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 11

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