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- PDB-1jhi: Solution Structure of a Hedamycin-DNA complex -

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Basic information

Entry
Database: PDB / ID: 1jhi
TitleSolution Structure of a Hedamycin-DNA complex
Components5'-D(*AP*CP*CP*(HEH)GP*GP*T)-3'
KeywordsDNA / Duplex DNA / HEDAMYCIN
Function / homologyHEDAMYCIN / DNA
Function and homology information
MethodSOLUTION NMR / Full relaxation matrix refinement Restrained Molecular Dynamics Torsion Angle dynamics
AuthorsOwen, E.A. / Burley, G.A. / Carver, J.A. / Wickham, G. / Keniry, M.A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Structural investigation of the hedamycin:d(ACCGGT)2 complex by NMR and restrained molecular dynamics.
Authors: Owen, E.A. / Burley, G.A. / Carver, J.A. / Wickham, G. / Keniry, M.A.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_leaving_atom_flag / _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 / pdbx_nmr_software
Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*AP*CP*CP*(HEH)GP*GP*T)-3'
B: 5'-D(*AP*CP*CP*(HEH)GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3673
Polymers3,6182
Non-polymers7491
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 / 100The 10 structures submitted are those with the lowest energy,and agree best with the NMR data.
RepresentativeModel #7

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Components

#1: DNA chain 5'-D(*AP*CP*CP*(HEH)GP*GP*T)-3'


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Hedamycin-DNA
#2: Chemical ChemComp-HEH / HEDAMYCIN


Mass: 748.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H52N2O11 / Comment: anticancer, antibiotic*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
122DQF-COSY
NMR detailsText: The data was collected and processed using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
1hedamycin covalently bound to G4 of d(ACCGGT)pH6.7 10%D2O/90%D2O buffer , 10mM phosphate, 50 mM NaCl
2hedamycin covalently bound to G4 of d(ACCGGT)pH6.7 100%D2O buffer , 10mM phosphate, 50 mM NaCl
Sample conditionsIonic strength: 0.05 / pH: 6.7 / Pressure: ambient / Temperature: 288 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
MARDIGRAS3.2Borgais, B. and James, T.L.iterative matrix relaxation
CHARMM23.2MOLECULAR SIMULATIONS INCORPORATED, Waltham MArefinement
CNSSOLVE1Brunger,A.T., Adams,P.D., Clore,G.M., DeLano,W.L., Gros,P. Grosse-Kunstleve,R.W., Jiang,T-S., Kuszewski,J., Nilges,M., Pannu,N.S., Read,R.J., Rice,L.M., Simonson,T., Warren,G.L.refinement
CORMA5.2Keepers,J. and James, T. L.refinement
VNMR6.1Varian Associatescollection
XEASY1.3.10Bartels,C, Xia, T-H, Billeter, M., Guntert,P & Wuthrich,data analysis
RefinementMethod: Full relaxation matrix refinement Restrained Molecular Dynamics Torsion Angle dynamics
Software ordinal: 1
NMR ensembleConformer selection criteria: The 10 structures submitted are those with the lowest energy,and agree best with the NMR data.
Conformers calculated total number: 100 / Conformers submitted total number: 10

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