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- PDB-1jo1: N7-Guanine Adduct of 2,7-diaminomitosene with DNA -

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Basic information

Entry
Database: PDB / ID: 1jo1
TitleN7-Guanine Adduct of 2,7-diaminomitosene with DNA
Components5'-D(*GP*TP*GP*(DAJ)GP*TP*AP*TP*AP*CP*CP*AP*C)-3'
KeywordsDNA / double helix / major groove binding drug / guanine-N7-alkylator
Function / homologyDECARBAMOYL-2,7-DIAMINOMITOSENE / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, molecular dynamics
AuthorsSubramaniam, G. / Paz, M.M. / Kumar, G.S. / Das, A. / Palom, Y. / Clement, C.C. / Patel, D.J. / Tomasz, M.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure of a guanine-N7-linked complex of the mitomycin C metabolite 2,7-diaminomitosene and DNA. Basis of sequence selectivity.
Authors: Subramaniam, G. / Paz, M.M. / Suresh Kumar, G. / Das, A. / Palom, Y. / Clement, C.C. / Patel, D.J. / Tomasz, M.
History
DepositionJul 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: 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: 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_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 / _struct_conn.pdbx_leaving_atom_flag / _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(*GP*TP*GP*(DAJ)GP*TP*AP*TP*AP*CP*CP*AP*C)-3'
B: 5'-D(*GP*TP*GP*(DAJ)GP*TP*AP*TP*AP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8174
Polymers7,3252
Non-polymers4932
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 12lowest number of NOE violations
Representative

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Components

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


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized using ABI-380B synthesizer
#2: Chemical ChemComp-DAJ / DECARBAMOYL-2,7-DIAMINOMITOSENE


Mass: 246.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N3O2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
132P-COSY
142HOHAHA
252P-COSY
2622D NOESY
NMR detailsText: This structure was determined using standard 2d-NOE buildup studies in H2O and D2O buffers.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM d(GTG(+G)TATACCAC) duplex in 0.01 M sodium phosphate, 0.1 M NaCl, 0.001M EDTA90% H2O/10% D2O
21.2 mM d(GTG(+G)TATACCAC) duplex in 0.01 M sodium phosphate, 0.1 M NaCl, 0.001M EDTA100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NaCl 6.8 ambient 278 K
20.1 M NaCl 6.8 ambient 303 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
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Instrumentscollection
Felix3MSIdata analysis
X-PLOR3.01A. Brungerstructure solution
X-PLOR3.01A. Brungerrefinement
RefinementMethod: distance geometry, molecular dynamics / Software ordinal: 1
Details: The structure is based on 126 intramolecular DNA constraints, 30 H-bonding constraints, 48 intermolecular drug-DNA constraints, and 48 dihedral constraints
NMR ensembleConformer selection criteria: lowest number of NOE violations
Conformers calculated total number: 12 / Conformers submitted total number: 1

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