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- PDB-1r4e: Solution structure of the Complex Formed between a Left-Handed We... -

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Basic information

Entry
Database: PDB / ID: 1r4e
TitleSolution structure of the Complex Formed between a Left-Handed Wedge-Shaped Spirocyclic Molecule and Bulged DNA
Components
  • 5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3'
  • 5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3'
KeywordsDNA / Wedge-shaped spirocyclic enantiomer-bulged DNA complex
Function / homologyChem-DDI / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsHwang, G.S. / Jones, G.B. / Goldberg, I.H.
CitationJournal: Biochemistry / Year: 2004
Title: Stereochemical control of small molecule binding to bulged DNA: comparison of structures of spirocyclic enantiomer-bulged DNA complexes.
Authors: Hwang, G.S. / Jones, G.B. / Goldberg, I.H.
History
DepositionOct 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3'
B: 5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4903
Polymers7,9602
Non-polymers5301
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 / 10all calculated structures submitted
RepresentativeModel #1all calculated structures submited have the least restraint violation and the lowst energy.

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Components

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


Mass: 4265.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by DNA synthesizer.
#2: DNA chain 5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3'


Mass: 3694.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by DNA synthesizer.
#3: Chemical ChemComp-DDI / SPIRO[NAPHTHALENE-2(3H),3'(10'H)-PENTALENO[1,2-B]NAPHTHALENE]-3,10'-DIONE, 2'-[(2-AMINO-2-DEOXY-B-D-GULOPYRANOSYL)OXY]-1,1',2',3'A,4,10'A-HEXAHYDRO-,(2'R,3'AS,10'AR)-(9CI)


Mass: 529.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H31NO7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141H-P CPSY
NMR detailsText: This structure was determined using 2D homonuclear and heteronuclear techniques.

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Sample preparation

DetailsContents: 1.2 mM ent-DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer, 90% H2O/10% D2O, 99.96% D2O
Solvent system: 90% H2O/10% D2O; 99.96% D2O
Sample conditionsIonic strength: 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer
pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2002.044.17.08Delaglio, F.processing
Sparky3.106Goddard, T.D. and Kneller. D.G.data analysis
CNS1Brunger, A.T. et alrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 427 NOE restraints and 166 dihedral angle restraints.
NMR representativeSelection criteria: all calculated structures submited have the least restraint violation and the lowst energy.
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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