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- PDB-1l0r: NMR Solution Structure of Nogalamycin Intercalation Between Co-Ax... -

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Basic information

Entry
Database: PDB / ID: 1l0r
TitleNMR Solution Structure of Nogalamycin Intercalation Between Co-Axially Stacked Hairpins
Components5'-D(*AP*CP*GP*AP*AP*GP*TP*GP*CP*GP*AP*AP*GP*C)-3'
KeywordsDNA / GAA loop / Single Strand Break / drug-DNA recognition / Nogalamycin intercalation
Function / homologyNOGALAMYCIN (PROTONATED FORM) / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics
AuthorsWilliams, H.E.L. / Colgrave, M.L. / Searle, M.S.
CitationJournal: Eur.J.Biochem. / Year: 2002
Title: Drug recognition of a DNA single strand break: nogalamycin intercalation between coaxially stacked hairpins.
Authors: Williams, H.E.L. / Colgrave, M.L. / Searle, M.S.
History
DepositionFeb 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,40614
Polymers4,3391
Non-polymers1,06713
Water39,5252194
1


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

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Components

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


Mass: 4338.843 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE WAS SYNTHESIZED BY Solid phase using phosphoramidite chemistry.
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NGP / NOGALAMYCIN (PROTONATED FORM)


Mass: 790.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H52NO16
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY with WATERGATE suppresion
131DQF-COSY
141TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM hairpin; 10mM phosphate, 100mM NaCl; 0.6mM NaN3; 0.6mM Na4 EDTA; 2mM Trimethylisilylpropanoate D2OD2O
23mM hairpin; 10mM phosphate, 100mM NaCl; 0.6mM NaN3; 0.6mM Na4 EDTA; 2mM Trimethylisilylpropanoate 10% D2O, 90% H2O10% D2O, 90% H2O
Sample conditionsIonic strength: 100mM Na+ 10mM PO4- / pH: 6.4 / Pressure: ATMOSPHERIC atm / Temperature: 278 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 AVANCE DRXBrukerAVANCE DRX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6-3.1collection
ANSIG3.3data analysis
Amber6structure solution
Amber6PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR ensembleConformers submitted total number: 1

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