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- PDB-1on5: SOLUTION STRUCTURE OF A CHOLIC ACID-CAPPED DNA DUPLEX -

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Basic information

Entry
Database: PDB / ID: 1on5
TitleSOLUTION STRUCTURE OF A CHOLIC ACID-CAPPED DNA DUPLEX
ComponentsSteroid-DNA hybrid
KeywordsDNA / steroid / synthetic hybrid
Function / homologyCHOLIC ACID / DNA
Function and homology information
MethodSOLUTION NMR / Torsion-Angle Molecular Dynamics
AuthorsTuma, J. / Richert, C.
CitationJournal: Biochemistry / Year: 2003
Title: Solution Structure of a Steroid-DNA Complex with Cholic Acid Residues Sealing the Termini of a Watson-Crick Duplex
Authors: Tuma, J. / Richert, C.
History
DepositionFeb 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Steroid-DNA hybrid
B: Steroid-DNA hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2744
Polymers3,4572
Non-polymers8172
Water00
1


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

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Components

#1: DNA chain Steroid-DNA hybrid


Mass: 1728.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesis of the DNA fragment by the authors.
#2: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY, DQF-COSY, TOCSY, HMQC, HMBC
2222D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1analyte buffer, saltD2O
2analyte buffer, saltH2O/D2O(85:15)
Sample
UnitsComponentSolution-ID
%analyte buffer, salt, D2O1
%analyte buffer, salt, H2O/D2O(85:15)2
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1165mM Phosphate buffer (KH2PO4/K2HPO4), NaCl at pH 7 (uncorrected for deuterium effect) 7 ambient 286 K
2165mM Phosphate buffer (KH2PO4/K2HPO4), NaCl at pH 7 (uncorrected for deuterium effect) 7 ambient 286 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: Torsion-Angle Molecular Dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers submitted total number: 1

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