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- PDB-1cyz: NMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1cyz
TitleNMR STRUCTURE OF THE GAACTGGTTC/TRI-IMIDAZOLE POLYAMIDE COMPLEX
Components5'-D(*GP*AP*AP*CP*TP*GP*GP*TP*TP*C)-3'
KeywordsDNA / T:G RECOGNIZED BY IM/IM PAIR IN THE DNA MINOR GROOVE
Function / homologyChem-AR1 / DNA
Function and homology information
MethodSOLUTION NMR / NOE-RESTRAINED CONJUGATE GRADIENT REFINEMENT IN X-PLOR; FULL MATRIX RELAXATION
AuthorsYang, X.-L. / Hubbard IV, R.B. / Lee, M. / Tao, Z.-F. / Sugiyama, H. / Wang, A.H.-J.
Citation
Journal: Nucleic Acids Res. / Year: 1999
Title: Imidazole-imidazole pair as a minor groove recognition motif for T:G mismatched base pairs
Authors: Yang, X.-L. / Hubbard IV, R.B. / Lee, M. / Tao, Z.-F. / Sugiyama, H. / Wang, A.H.-J.
#1: Journal: Eur.J.Biochem. / Year: 1999
Title: Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy
Authors: Yang, X.-L. / Kaenzig, C. / Lee, M. / Wang, A.H.-J.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,0934
Polymers6,1202
Non-polymers9732
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 11REFINED AVERAGE STRUCTURE
RepresentativeModel #1refined average structure

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Components

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


Mass: 3060.016 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-AR1 / (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1 H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM / TRI-IMIDAZOLE DNA MINOR GROOVE BINDER / AR-1-144


Mass: 486.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N11O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR TECHNIQUES WITH BACK NOE CALCULATION

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Sample preparation

DetailsContents: 1.5 MM DNA DUPLEX; 20 MM PHOSPHATE BUFFER; 100% D2O OR 90% H2O, 10% D2O
Sample conditionsIonic strength: NO ADDITIONAL SALT / pH: 7 / Pressure: AMBIENT / Temperature: 275 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix1.1 AND 98MSIdata analysis
X-PLOR3.851BRUNGERrefinement
RefinementMethod: NOE-RESTRAINED CONJUGATE GRADIENT REFINEMENT IN X-PLOR; FULL MATRIX RELAXATION
Software ordinal: 1
NMR representativeSelection criteria: refined average structure
NMR ensembleConformer selection criteria: REFINED AVERAGE STRUCTURE / Conformers calculated total number: 11 / Conformers submitted total number: 1

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