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- PDB-2oey: Solution Structure of a Designed Spirocyclic Helical Ligand Bindi... -

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Basic information

Entry
Database: PDB / ID: 2oey
TitleSolution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA
ComponentsDNA (25-MER)
KeywordsDNA / Designed spirocyclic helical ligand-bulged DNA complex
Function / homologyChem-S2A / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsZhang, N. / Lin, Y. / Xiao, Z. / Jones, G.B. / Goldberg, I.H.
Citation
Journal: Biochemistry / Year: 2007
Title: Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA.
Authors: Zhang, N. / Lin, Y. / Xiao, Z. / Jones, G.B. / Goldberg, I.H.
#1: Journal: Science / Year: 1996
Title: Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analogue
Authors: Stassinopoulos, A. / Ji, J. / Gao, X. / Goldberg, I.H.
#2: Journal: Biochemistry / Year: 2002
Title: Induced formation of a DNA bulge structure by a molecular wedge ligand-post activated neocarzinostatin chromophore
Authors: Gao, X. / Stassinopolous, A. / Ji, J. / Kwon, Y. / Bare, S. / Goldberg, I.H.
History
DepositionJan 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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 / 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 1.4Dec 27, 2023Group: 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 (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2212
Polymers7,6811
Non-polymers5401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: DNA chain DNA (25-MER)


Mass: 7680.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This is an artifical sequence
#2: Chemical ChemComp-S2A / (1R,3A'S,10'S,10A'R)-7-METHOXY-2-OXO-10',10A'-DIHYDRO-2H,3A'H-SPIRO[NAPHTHALENE-1,3'-PENTALENO[1,2-B]NAPHTHALEN]-10'-YL 2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE / SPIROCYCLIC ALKENE


Mass: 539.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H33NO6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1322D TOCSY
142DQF-COSY
NMR detailsText: This structure was determined using standard methods for DNA-drug complex.

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Sample preparation

Details
Solution-IDContentsSolvent system
110mM phosphate buffer; 100 mM NaCl90% H2O/10% D2O
210mM phosphate buffer; 100 mM NaCl100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 6.8ambient 273 K
2100 mM NaCl 6.8ambient 283 K
3100 mM NaCl 6.8ambient 298 K
4100 mM NaCl 6.8ambient 303 K

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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
X-PLOR3.851Brugerrefinement
Felix2000data analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: the structures are based on a total of 531 restraints, 506 are NOE-derived distance constraints, 25 dihedral angle restraints,40 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 8

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