data_5717 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR STRUCTURE OF THE CK14 DNA DUPLEX: A PORTION OF THE KNOWN NF-kB SEQUENCE CK1 ; _BMRB_accession_number 5717 _BMRB_flat_file_name bmr5717.str _Entry_type new _Submission_date 2003-03-04 _Accession_date 2003-03-05 _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 Volk D. E. . 2 Yang X. . . 3 Fennewald S. M. . 4 King D. . . 5 Bassett Suzanne E. . 6 Venkitachalam S. . . 7 Herzog N. . . 8 Luxon B. A. . 9 Gorenstein D. G. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 100 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2003-04-30 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 5716 'CK14 DNA 14-MER DUPLEX' 5718 'XBY2 DNA 14-MER DUPLEX' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure and Design of Dithiophosphate Backbone Aptamers Targeting Transcription Factor NF-kB ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Volk David E. . 2 Yang Xianbin . . 3 Fennewald Susan M. . 4 King David J. . 5 Bassett Suzanne E. . 6 Venkitachalam Sheela . . 7 Herzog Norbert . . 8 Luxon Bruce A. . 9 Gorenstein David G. . stop_ _Journal_abbreviation 'Bioorg. Chem.' _Journal_volume 30 _Journal_issue 6 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 396 _Page_last 419 _Year 2002 _Details . loop_ _Keyword 'DNA DUPLEX' CK14 CK1 NF-KB thiophosphate dithiophosphate stop_ save_ ################################## # Molecular system description # ################################## save_system_XBY6 _Saveframe_category molecular_system _Mol_system_name 'XBY6 DNA 14-MER DUPLEX' _Abbreviation_common XBY6 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label XBY6A $XBY6A XBY6B $XBY6B stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_XBY6A _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common XBY6A _Abbreviation_common XBY6A _Molecular_mass . _Mol_thiol_state 'not present' _Details 'XBY6 Strand A has phosphordithioate substitutions at positions T10 and C11' ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence CCAGGAGATTCCAC loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DA 4 DG 5 DG 6 DA 7 DG 8 DA 9 DT 10 DT 11 DC 12 DC 13 DA 14 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_XBY6B _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common XBY6B _Abbreviation_common XBY6B _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 14 _Mol_residue_sequence GTGGAATCTCCTGG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 12 DG 2 13 DT 3 14 DG 4 15 DG 5 16 DA 6 17 DA 7 18 DT 8 29 DC 9 20 DT 10 21 DC 11 22 DC 12 23 DT 13 24 DG 14 25 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $XBY6A 'E. Coli' 562 Eubacteria . Escherichia coli $XBY6B 'E. Coli' 562 Eubacteria . Escherichia coli 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 _Details $XBY6A 'chemical synthesis' . . . . . ; Thiophosphoramidite chemistry was used to synthesize dithio substitutions ; $XBY6B 'chemical synthesis' . . . . . ; Thiophosphoramidite chemistry was used to synthesize dithio substitutions ; 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 $XBY6A . mM 0.5 1.0 . $XBY6B . mM 0.5 1.0 . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $XBY6A . mM 0.5 1.0 . $XBY6B . mM 0.5 1.0 . Phosphate 20 mM . . . NaCl 56 mM . . . NaN3 50 mM . . . D2O 99.96 % . . . stop_ save_ ############################ # Computer software used # ############################ save_MORASS _Saveframe_category software _Name MORASS _Version 2.5 loop_ _Task 'iterative matrix relaxation' stop_ _Details 'Total Relation Matrix Program' save_ save_AMBER _Saveframe_category software _Name AMBER _Version 5 loop_ _Task 'molecular dynamics calculations' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITYplus _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label . save_ save_2D_Exchange_Spectroscopy_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Exchange Spectroscopy' _Sample_label . save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Exchange Spectroscopy' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.7 0.2 n/a temperature 278 1 K 'ionic strength' 100 0.02 mM pressure 1 . atm stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.7 0.2 n/a temperature 288 1 K 'ionic strength' 100 0.02 mM pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_2 stop_ _Sample_conditions_label $sample_cond_2 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name XBY6B _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 . 1 DG H8 H 7.95 0.01 1 2 . 1 DG H1' H 6.00 0.01 1 3 . 1 DG H2' H 2.60 0.01 1 4 . 1 DG H2'' H 2.77 0.01 1 5 . 1 DG H3' H 5.13 0.01 1 6 . 1 DG H4' H 4.28 0.01 1 7 . 2 DT H6 H 7.35 0.01 1 8 . 2 DT H71 H 1.41 0.01 1 9 . 2 DT H72 H 1.41 0.01 1 10 . 2 DT H73 H 1.41 0.01 1 11 . 2 DT H1' H 5.52 0.01 1 12 . 2 DT H2' H 2.15 0.01 1 13 . 2 DT H2'' H 2.43 0.01 1 14 . 2 DT H3' H 5.09 0.01 1 15 . 2 DT H4' H 4.23 0.01 1 16 . 3 DG H8 H 8.02 0.01 1 17 . 3 DG H1' H 5.70 0.01 1 18 . 3 DG H2' H 2.65 0.01 1 19 . 3 DG H2'' H 2.76 0.01 1 20 . 3 DG H3' H 4.99 0.01 1 21 . 3 DG H4' H 4.40 0.01 1 22 . 4 DG H8 H 7.68 0.01 1 23 . 4 DG H1' H 5.45 0.01 1 24 . 4 DG H2' H 2.55 0.01 1 25 . 4 DG H2'' H 2.68 0.01 1 26 . 4 DG H3' H 4.99 0.01 1 27 . 4 DG H4' H 4.34 0.01 1 28 . 5 DA H2 H 7.29 0.01 1 29 . 5 DA H8 H 8.05 0.01 1 30 . 5 DA H1' H 5.94 0.01 1 31 . 5 DA H2' H 2.66 0.01 1 32 . 5 DA H2'' H 2.89 0.01 1 33 . 5 DA H3' H 5.04 0.01 1 34 . 5 DA H4' H 4.43 0.01 1 35 . 6 DA H8 H 8.07 0.01 1 36 . 6 DA H1' H 6.13 0.01 1 37 . 6 DA H2' H 2.54 0.01 1 38 . 6 DA H2'' H 2.84 0.01 1 39 . 6 DA H3' H 4.96 0.01 1 40 . 6 DA H4' H 4.43 0.01 1 41 . 7 DT H6 H 7.12 0.01 1 42 . 7 DT H71 H 1.30 0.01 1 43 . 7 DT H72 H 1.30 0.01 1 44 . 7 DT H73 H 1.30 0.01 1 45 . 7 DT H1' H 5.69 0.01 1 46 . 7 DT H2' H 2.17 0.01 1 47 . 7 DT H2'' H 2.43 0.01 1 48 . 7 DT H3' H 5.05 0.01 1 49 . 7 DT H4' H 4.28 0.01 1 50 . 8 DC H5 H 5.52 0.01 1 51 . 8 DC H6 H 7.67 0.01 1 52 . 8 DC H1' H 5.95 0.01 1 53 . 8 DC H2' H 2.17 0.01 1 54 . 8 DC H2'' H 2.56 0.01 1 55 . 8 DC H3' H 4.68 0.01 1 56 . 8 DC H4' H 4.26 0.01 1 57 . 9 DT H6 H 7.53 0.01 1 58 . 9 DT H71 H 1.62 0.01 1 59 . 9 DT H72 H 1.62 0.01 1 60 . 9 DT H73 H 1.62 0.01 1 61 . 9 DT H1' H 5.87 0.01 1 62 . 9 DT H2' H 2.26 0.01 1 63 . 9 DT H2'' H 2.54 0.01 1 64 . 9 DT H3' H 5.15 0.01 1 65 . 9 DT H4' H 4.25 0.01 1 66 . 10 DC H5 H 5.68 0.01 1 67 . 10 DC H6 H 7.71 0.01 1 68 . 10 DC H1' H 6.01 0.01 1 69 . 10 DC H2' H 2.23 0.01 1 70 . 10 DC H2'' H 2.51 0.01 1 71 . 10 DC H3' H 4.83 0.01 1 72 . 10 DC H4' H 4.23 0.01 1 73 . 11 DC H5 H 5.61 0.01 1 74 . 11 DC H6 H 7.55 0.01 1 75 . 11 DC H1' H 5.88 0.01 1 76 . 11 DC H2' H 2.03 0.01 1 77 . 11 DC H2'' H 2.39 0.01 1 78 . 11 DC H3' H 4.81 0.01 1 79 . 11 DC H4' H 4.14 0.01 1 80 . 12 DT H6 H 7.41 0.01 1 81 . 12 DT H71 H 1.70 0.01 1 82 . 12 DT H72 H 1.70 0.01 1 83 . 12 DT H73 H 1.70 0.01 1 84 . 12 DT H1' H 5.31 0.01 1 85 . 12 DT H2' H 2.08 0.01 1 86 . 12 DT H2'' H 2.27 0.01 1 87 . 12 DT H3' H 5.03 0.01 1 88 . 12 DT H4' H 4.15 0.01 1 89 . 13 DG H8 H 8.14 0.01 1 90 . 13 DG H1' H 5.79 0.01 1 91 . 13 DG H2' H 2.73 0.01 1 92 . 13 DG H2'' H 2.78 0.01 1 93 . 13 DG H3' H 5.00 0.01 1 94 . 13 DG H4' H 4.42 0.01 1 95 . 14 DG H8 H 7.83 0.01 1 96 . 14 DG H1' H 6.13 0.01 1 97 . 14 DG H2' H 2.57 0.01 1 98 . 14 DG H2'' H 2.35 0.01 1 99 . 14 DG H3' H 4.68 0.01 1 100 . 14 DG H4' H 4.20 0.01 1 stop_ save_