data_17094 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR and molecular modeling studies of the interaction of berenil and pentamidine with d(CGCAAATTTGCG)2 ; _BMRB_accession_number 17094 _BMRB_flat_file_name bmr17094.str _Entry_type new _Submission_date 2010-08-02 _Accession_date 2010-08-02 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jenkins Terence C. . 2 Lane Andrew N. . 3 Neidle Stephen . . 4 Brown David G. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count kinetic_rates 1 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-11-10 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR and molecular modeling studies of the interaction of berenil and pentamidine with d(CGCAAATTTGCG)2' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8504811 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Jenkins Terence C. . 2 Lane Andrew N. . 3 Neidle Stephen . . 4 Brown David G. . stop_ _Journal_abbreviation 'Eur. J. Biochem.' _Journal_name_full 'European Journal of Biochemistry' _Journal_volume 213 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1175 _Page_last 1184 _Year 1993 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'DNA 1/berenil complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA 1' $DNA_1 berenil $BRN stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CGCAAATTTGCG loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DA 5 DA 6 DA 7 DT 8 DT 9 DT 10 DG 11 DC 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_BRN _Saveframe_category ligand _Mol_type non-polymer _Name_common "BRN (BERENIL)" _BMRB_code . _PDB_code BRN _Molecular_mass 281.316 _Mol_charge 0 _Mol_paramagnetic no _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Jun 9 13:15:10 2009 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? NA NA N . 0 . ? NB NB N . 0 . ? N1 N1 N . 0 . ? N N N . 0 . ? N1' N1' N . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4' C4' C . 0 . ? C5' C5' C . 0 . ? C6' C6' C . 0 . ? C7' C7' C . 0 . ? NA' NA' N . 0 . ? NB' NB' N . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HN1 HN1 H . 0 . ? H2' H2' H . 0 . ? H3' H3' H . 0 . ? H5' H5' H . 0 . ? H6' H6' H . 0 . ? HA' HA' H . 0 . ? HB'1 HB'1 H . 0 . ? HB'2 HB'2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB C1 C2 ? ? SING C1 C6 ? ? SING C1 N1 ? ? SING C2 C3 ? ? SING C2 H2 ? ? DOUB C3 C4 ? ? SING C3 H3 ? ? SING C4 C5 ? ? SING C4 C7 ? ? DOUB C5 C6 ? ? SING C5 H5 ? ? SING C6 H6 ? ? DOUB C7 NA ? ? SING C7 NB ? ? SING NA HA ? ? SING NB HB1 ? ? SING NB HB2 ? ? SING N1 N ? ? SING N1 HN1 ? ? DOUB N N1' ? ? SING N1' C1' ? ? DOUB C1' C2' ? ? SING C1' C6' ? ? SING C2' C3' ? ? SING C2' H2' ? ? DOUB C3' C4' ? ? SING C3' H3' ? ? SING C4' C5' ? ? SING C4' C7' ? ? DOUB C5' C6' ? ? SING C5' H5' ? ? SING C6' H6' ? ? DOUB C7' NA' ? ? SING C7' NB' ? ? SING NA' HA' ? ? SING NB' HB'1 ? ? SING NB' HB'2 ? ? stop_ _Mol_thiol_state 'not present' _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $DNA_1 . . . . . . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $DNA_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $DNA_1 1.0 mM . . 'natural abundance' $BRN . uM 0 1200 'natural abundance' 'potassium chloride' 100 mM . . 'natural abundance' 'sodium phosphate' 10 mM . . 'natural abundance' EDTA 0.2 mM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NUCFIT _Saveframe_category software _Name NUCFIT _Version . loop_ _Vendor _Address _Electronic_address '(Lane, A.N. 1990)' . . stop_ loop_ _Task 'NOE processing' stop_ _Details . save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 2.1 loop_ _Vendor _Address _Electronic_address Brunger . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_AMPAC _Saveframe_category software _Name AMPAC _Version . loop_ _Vendor _Address _Electronic_address '(Quantum Chemistry Program Exchange, QCPE-506)' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AM _Field_strength 400 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model Unity _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 303 . K pD 7.0 . pH pressure 1 . atm stop_ save_