data_4243 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Intercalated d(TCCCGTTTCCA) dimer ; _BMRB_accession_number 4243 _BMRB_flat_file_name bmr4243.str _Entry_type original _Submission_date 1998-10-13 _Accession_date 1998-10-13 _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 GALLEGO JOSE . . 2 CHOU SHAN-HO . . 3 REID BRIAN R. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 84 "31P chemical shifts" 10 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 2000-05-01 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Centromeric pyrimidine strands fold into an intercalated motif by forming a double hairpin with a novel T:G:G:T tetrad: solution structure of the D(TCCCGTTTCCA) dimer ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 98035724 _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 GALLEGO JOSE . . 2 CHOU SHAN-HO . . 3 REID BRIAN R. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of Molecular Biology' _Journal_volume 273 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 840 _Page_last 856 _Year 1997 _Details . loop_ _Keyword 'Deoxyribonucleic acid' 'Alphoid DNA' Centromere Hairpin I-motif 'TGGT Tetrad' stop_ save_ ####################################### # Cited references within the entry # ####################################### save_citation_one _Saveframe_category citation _Citation_full ; Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. J. Biomol. NMR 6, 135-140 (1995). ; _Citation_title '1H, 13C and 15N chemical shift referencing in biomolecular NMR.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 8589602 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wishart 'D S' S. . 2 Bigam 'C G' G. . 3 Yao J . . 4 Abildgaard F . . 5 Dyson 'H J' J. . 6 Oldfield E . . 7 Markley 'J L' L. . 8 Sykes 'B D' D. . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_name_full 'Journal of biomolecular NMR' _Journal_volume 6 _Journal_issue 2 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 135 _Page_last 140 _Year 1995 _Details ; A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here. ; save_ ################################## # Molecular system description # ################################## save_i-motif _Saveframe_category molecular_system _Mol_system_name 'DNA (5'-D(TCCCGTTTCCA)-3')' _Abbreviation_common i-motif _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA monomer 1' $DNA_1 'DNA monomer 2' $DNA_1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Magnetic_equivalence_ID _Magnetically_equivalent_system_component 1 'DNA monomer 1' 1 'DNA monomer 2' stop_ _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 _Name_variant 'DNA (5'-D(TCCCGTTTCCA)-3')' _Abbreviation_common 'DNA (5'-D(TCCCGTTTCCA)-3')' _Molecular_mass . _Mol_thiol_state 'not present' _Details ; The cytosines of one of the monomers are protonated and are labeled with "+C" i-motif ; ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence TCCCGTTTCCA loop_ _Residue_seq_code _Residue_label 1 DT 2 DC 3 DC 4 DC 5 DG 6 DT 7 DT 8 DT 9 DC 10 DC 11 DA 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 _Details $DNA_1 human 9606 Eukaryota Metazoa Homo sapiens 'alphoid DNA from centromere of human chromosomes"' 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_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $DNA_1 3.9 mM . stop_ save_ ############################ # Computer software used # ############################ save_software_one _Saveframe_category software _Name FELIX _Version 2.30 _Details . save_ save_software_two _Saveframe_category software _Name DISCOVER _Version . _Details . save_ save_software_three _Saveframe_category software _Name AMBER _Version 4.0 _Details . save_ save_software_four _Saveframe_category software _Name BIRDER _Version . loop_ _Task 'relaxation matrix simulation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_one _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ save_NMR_spectrometer_two _Saveframe_category NMR_spectrometer _Manufacturer Home-built _Model . _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_1D_H_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D H' _Sample_label $sample_one save_ save_1D_P_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1D P' _Sample_label $sample_one save_ save_2D_H/H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D H/H NOESY' _Sample_label $sample_one save_ save_H/H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'H/H COSY' _Sample_label $sample_one save_ save_H/P_HETCOR_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'H/P HETCOR' _Sample_label $sample_one save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D H' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '1D P' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D H/H NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name 'H/H COSY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_5 _Saveframe_category NMR_applied_experiment _Experiment_name 'H/P HETCOR' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.1 0.1 n/a temperature 302 0.1 K 'ionic strength' 0.2 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_one _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 HDO H 1 'water proton' ppm 4.6 . direct . internal . trimethylphosphate P 31 phosphorus ppm 0 . direct . external . 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_assigned_chemical_shifts _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Chem_shift_reference_set_label $chemical_shift_reference_one _Mol_system_component_name 'DNA monomer 1' _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 DT H6 H 7.58 . 1 2 . 1 DT H71 H 1.72 . 1 3 . 1 DT H72 H 1.72 . 1 4 . 1 DT H73 H 1.72 . 1 5 . 1 DT H1' H 6.17 . 1 6 . 1 DT H2' H 2.32 . 1 7 . 1 DT H2'' H 2.48 . 1 8 . 1 DT H3' H 4.75 . 1 9 . 1 DT H4' H 4.15 . 1 10 . 2 DC H5 H 5.91 . 1 11 . 2 DC H6 H 7.71 . 1 12 . 2 DC H1' H 5.72 . 1 13 . 2 DC H2' H 1.87 . 1 14 . 2 DC H2'' H 2.33 . 1 15 . 2 DC H3' H 4.79 . 1 16 . 2 DC H4' H 4.14 . 1 17 . 2 DC P P -4.02 . 1 18 . 3 DC H5 H 5.86 . 1 19 . 3 DC H6 H 7.7 . 1 20 . 3 DC H1' H 6.33 . 1 21 . 3 DC H2' H 2.07 . 1 22 . 3 DC H2'' H 2.51 . 1 23 . 3 DC H3' H 4.65 . 1 24 . 3 DC H4' H 4.06 . 1 25 . 3 DC P P -4.07 . 1 26 . 4 DC H5 H 5.88 . 1 27 . 4 DC H6 H 7.48 . 1 28 . 4 DC H1' H 6.16 . 1 29 . 4 DC H2' H 1.07 . 1 30 . 4 DC H2'' H 2.07 . 1 31 . 4 DC H3' H 4.51 . 1 32 . 4 DC H4' H 4.2 . 1 33 . 4 DC P P -3.42 . 1 34 . 5 DG H8 H 8.25 . 1 35 . 5 DG H1' H 5.94 . 1 36 . 5 DG H2' H 2.94 . 1 37 . 5 DG H2'' H 2.65 . 1 38 . 5 DG H3' H 5.09 . 1 39 . 5 DG H4' H 4.33 . 1 40 . 5 DG P P -5.2 . 1 41 . 6 DT H6 H 7.62 . 1 42 . 6 DT H71 H 1.73 . 1 43 . 6 DT H72 H 1.73 . 1 44 . 6 DT H73 H 1.73 . 1 45 . 6 DT H1' H 6.06 . 1 46 . 6 DT H2' H 2.06 . 1 47 . 6 DT H2'' H 2.3 . 1 48 . 6 DT H3' H 4.8 . 1 49 . 6 DT H4' H 3.83 . 1 50 . 6 DT P P -4.67 . 1 51 . 7 DT H6 H 7.79 . 1 52 . 7 DT H71 H 1.89 . 1 53 . 7 DT H72 H 1.89 . 1 54 . 7 DT H73 H 1.89 . 1 55 . 7 DT H1' H 6.43 . 1 56 . 7 DT H2' H 2.22 . 1 57 . 7 DT H2'' H 2.55 . 1 58 . 7 DT H3' H 4.6 . 1 59 . 7 DT H4' H 4.51 . 1 60 . 7 DT P P -4.21 . 1 61 . 8 DT H6 H 7.91 . 1 62 . 8 DT H71 H 2.02 . 1 63 . 8 DT H72 H 2.02 . 1 64 . 8 DT H73 H 2.02 . 1 65 . 8 DT H1' H 6.43 . 1 66 . 8 DT H2' H 2.51 . 2 67 . 8 DT H2'' H 2.51 . 2 68 . 8 DT H3' H 4.93 . 1 69 . 8 DT H4' H 4.35 . 1 70 . 8 DT P P -4.3 . 1 71 . 9 DC H5 H 6.02 . 1 72 . 9 DC H6 H 7.85 . 1 73 . 9 DC H1' H 6.45 . 1 74 . 9 DC H2' H 2.04 . 1 75 . 9 DC H2'' H 2.51 . 1 76 . 9 DC H3' H 4.94 . 1 77 . 9 DC H4' H 4.32 . 1 78 . 9 DC P P -3.3 . 1 79 . 10 DC H5 H 5.85 . 1 80 . 10 DC H6 H 7.59 . 1 81 . 10 DC H1' H 6.23 . 1 82 . 10 DC H2' H 2.06 . 1 83 . 10 DC H2'' H 2.22 . 1 84 . 10 DC H3' H 4.58 . 1 85 . 10 DC H4' H 4.01 . 1 86 . 10 DC P P -3.37 . 1 87 . 11 DA H2 H 7.89 . 1 88 . 11 DA H8 H 8.26 . 1 89 . 11 DA H1' H 6.35 . 1 90 . 11 DA H2' H 2.65 . 1 91 . 11 DA H2'' H 2.49 . 1 92 . 11 DA H3' H 4.65 . 1 93 . 11 DA H4' H 4.17 . 1 94 . 11 DA P P -3.65 . 1 stop_ save_