data_4618 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The Solution Structure of [d(CGC)r(aaa)d(TTTGCG)]2: Hybrid Junctions Flanked by DNA Duplexes ; _BMRB_accession_number 4618 _BMRB_flat_file_name bmr4618.str _Entry_type original _Submission_date 2000-03-26 _Accession_date 2000-09-07 _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 Hsu S. T. . 2 Chou M. -T. . 3 Cheng J. -W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 104 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-19 update BMRB 'update DNA residue label to two-letter code' 2000-12-06 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Hydration of [d(CGC)r(aaa)d(TTTGCG)]2' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 20120850 _PubMed_ID 10653692 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hsu S. T. . 2 Chou M. -T. . 3 Chou S. -H. . 4 Huang W. -C. . 5 Cheng J. -W. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 295 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1129 _Page_last 1137 _Year 2000 _Details . loop_ _Keyword 'DNA/RNA Hybrid' 'Chimeric Duplex' stop_ save_ ################################## # Molecular system description # ################################## save_(CGCaaaTTTGCG)2 _Saveframe_category molecular_system _Mol_system_name DNA _Abbreviation_common (CGCaaaTTTGCG)2 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label CGCaaaTTTGCG-a $CGCaaaTTTGCG CGCaaaTTTGCG-b $CGCaaaTTTGCG stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state 'double strand' _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 CGCaaaTTTGCG-a 1 CGCaaaTTTGCG-b stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_CGCaaaTTTGCG _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA _Abbreviation_common (CGCaaaTTTGCG)2 _Molecular_mass . _Mol_thiol_state 'not present' _Details 'DNA/RNA hybrid : (5'-D(CpGpCp)-R(ApApAp)-D(TpTpTpGpCpG)-3')' ############################## # 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_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $CGCaaaTTTGCG . . . . . . 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 $CGCaaaTTTGCG '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 _Isotopic_labeling $CGCaaaTTTGCG . mM . stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NMR_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NMR' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.0 . pH temperature 300 . K 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 . H 1 . ppm 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_chem_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name CGCaaaTTTGCG-a _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 DC H6 H 7.52 . . 2 . 1 DC H5 H 5.74 . . 3 . 1 DC H1' H 5.61 . . 4 . 1 DC H2' H 1.87 . . 5 . 1 DC H2'' H 2.32 . . 6 . 1 DC H3' H 4.62 . . 7 . 1 DC H4' H 3.99 . . 8 . 1 DC H41 H 8.09 . . 9 . 1 DC H42 H 6.99 . . 10 . 2 DG H8 H 7.87 . . 11 . 2 DG H1' H 5.79 . . 12 . 2 DG H2' H 2.59 . . 13 . 2 DG H2'' H 2.65 . . 14 . 2 DG H3' H 4.9 . . 15 . 2 DG H4' H 4.29 . . 16 . 2 DG H1 H 12.95 . . 17 . 3 DC H6 H 7.25 . . 18 . 3 DC H5 H 5.32 . . 19 . 3 DC H1' H 5.61 . . 20 . 3 DC H2' H 2.05 . . 21 . 3 DC H2'' H 2.29 . . 22 . 3 DC H3' H 4.78 . . 23 . 3 DC H4' H 4.55 . . 24 . 3 DC H41 H 8.27 . . 25 . 3 DC H42 H 6.42 . . 26 . 4 DA H8 H 8.14 . . 27 . 4 DA H2 H 6.87 . . 28 . 4 DA H1' H 5.68 . . 29 . 4 DA H2' H 4.82 . . 30 . 4 DA H3' H 4.13 . . 31 . 4 DA H4' H 4.46 . . 32 . 4 DA H61 H 7.65 . . 33 . 4 DA H62 H 6.31 . . 34 . 4 DA H2'' H 6.51 . . 35 . 5 DA H8 H 7.99 . . 36 . 5 DA H2 H 7.2 . . 37 . 5 DA H1' H 5.8 . . 38 . 5 DA H2' H 4.42 . . 39 . 5 DA H3' H 4.51 . . 40 . 5 DA H4' H 4.18 . . 41 . 5 DA H61 H 7.50 . . 42 . 5 DA H62 H 6.44 . . 43 . 5 DA H2'' H 6.77 . . 44 . 6 DA H8 H 7.62 . . 45 . 6 DA H2 H 7.71 . . 46 . 6 DA H1' H 5.64 . . 47 . 6 DA H2' H 4.28 . . 48 . 6 DA H3' H 4.42 . . 49 . 6 DA H4' H 4.19 . . 50 . 6 DA H61 H 7.47 . . 51 . 6 DA H62 H 6.81 . . 52 . 6 DA H2'' H 6.89 . . 53 . 7 DT H6 H 7.31 . . 54 . 7 DT H71 H 1.428 . . 55 . 7 DT H72 H 1.428 . . 56 . 7 DT H73 H 1.428 . . 57 . 7 DT H1' H 5.68 . . 58 . 7 DT H2' H 2.11 . . 59 . 7 DT H2'' H 2.51 . . 60 . 7 DT H3' H 4.56 . . 61 . 7 DT H4' H 4.14 . . 62 . 7 DT H3 H 14.05 . . 63 . 8 DT H6 H 7.56 . . 64 . 8 DT H71 H 1.68 . . 65 . 8 DT H72 H 1.68 . . 66 . 8 DT H73 H 1.68 . . 67 . 8 DT H1' H 6.1 . . 68 . 8 DT H2' H 2.15 . . 69 . 8 DT H2'' H 2.6 . . 70 . 8 DT H3' H 4.81 . . 71 . 8 DT H4' H 4.24 . . 72 . 8 DT H3 H 13.6 . . 73 . 9 DT H6 H 7.32 . . 74 . 9 DT H71 H 1.82 . . 75 . 9 DT H72 H 1.82 . . 76 . 9 DT H73 H 1.82 . . 77 . 9 DT H1' H 5.88 . . 78 . 9 DT H2' H 2.11 . . 79 . 9 DT H2'' H 2.43 . . 80 . 9 DT H3' H 4.87 . . 81 . 9 DT H4' H 4.13 . . 82 . 9 DT H3 H 13.19 . . 83 . 10 DG H8 H 7.8 . . 84 . 10 DG H1' H 5.77 . . 85 . 10 DG H2' H 2.55 . . 86 . 10 DG H2'' H 2.59 . . 87 . 10 DG H3' H 4.94 . . 88 . 10 DG H4' H 4.94 . . 89 . 10 DG H1 H 12.38 . . 90 . 11 DC H6 H 7.28 . . 91 . 11 DC H5 H 5.31 . . 92 . 11 DC H1' H 5.65 . . 93 . 11 DC H2' H 1.87 . . 94 . 11 DC H2'' H 2.27 . . 95 . 11 DC H3' H 4.78 . . 96 . 11 DC H4' H 4.13 . . 97 . 11 DC H41 H 8.24 . . 98 . 11 DC H42 H 6.56 . . 99 . 12 DG H8 H 7.87 . . 100 . 12 DG H1' H 6.06 . . 101 . 12 DG H2' H 2.29 . . 102 . 12 DG H2'' H 2.54 . . 103 . 12 DG H3' H 4.61 . . 104 . 12 DG H4' H 5.12 . . stop_ save_