data_5681 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; DIMERIC SOLUTION STRUCTURE OF THE CYCLIC OCTAMER CD(CGCTCATT) ; _BMRB_accession_number 5681 _BMRB_flat_file_name bmr5681.str _Entry_type original _Submission_date 2003-01-31 _Accession_date 2003-01-31 _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 Escaja N. . . 2 Gelpi J. L. . 3 Orozco M. . . 4 Rico M. . . 5 Pedroso E. . . 6 Gonzalez C. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 91 "31P chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 2003-08-07 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Four-stranded DNA Structure Stabilized by a Novel C:G:A:T Tetrad' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22619798 _PubMed_ID 12733903 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Escaja N. . . 2 Gelpi J. L. . 3 Orozco M. . . 4 Rico M. . . 5 Pedroso E. . . 6 Gonzalez C. . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 125 _Journal_issue 19 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5654 _Page_last 5662 _Year 2003 _Details . loop_ _Keyword BI-LOOP 'FOUR-STRANDED DNA' QUADRUPLEX 'UNUSUAL DNA' stop_ save_ ################################## # Molecular system description # ################################## save_system_cgctcatt _Saveframe_category molecular_system _Mol_system_name 'CYCLIC OLIGONUCLEOTIDE D(CGCTCATT)' _Abbreviation_common cgctcatt _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'CYCLIC OLIGONUCLEOTIDE D(CGCTCATT), chain 1' $CGCTCATT 'CYCLIC OLIGONUCLEOTIDE D(CGCTCATT), chain 2' $CGCTCATT 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 'CYCLIC OLIGONUCLEOTIDE D(CGCTCATT), chain 1' 1 'CYCLIC OLIGONUCLEOTIDE D(CGCTCATT), chain 2' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_CGCTCATT _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common D(CGCTCATT) _Abbreviation_common D(CGCTCATT) _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 8 _Mol_residue_sequence CGCTCATT loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DC 4 DT 5 DC 6 DA 7 DT 8 DT 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 $CGCTCATT . . . . . . 'This is a model compound. Natural sources are not relevant.' 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 $CGCTCATT '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 $CGCTCATT 5 mM . stop_ save_ ############################ # Computer software used # ############################ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Task 'iterative matrix relaxation' stop_ _Details 'T.L. James' save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task 'structure calculation' stop_ _Details 'P. Guntert' save_ save_AMBER _Saveframe_category software _Name AMBER _Version 5.1 loop_ _Task refinement stop_ _Details 'D. Pearlman' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_hetero_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'hetero COSY' _Sample_label $sample_1 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 DQF-COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name 'hetero 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 7.0 0.2 n/a pressure 1 . atm temperature 278 0.5 K 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 DSS P 31 'methyl protons' ppm 0.0 . indirect . . . 0.404808636 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_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 'CYCLIC OLIGONUCLEOTIDE D(CGCTCATT), chain 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 DC H41 H 7.30 . 1 2 . 1 DC H42 H 6.77 . 1 3 . 1 DC H6 H 7.98 . 1 4 . 1 DC H5 H 6.11 . 1 5 . 1 DC H1' H 6.49 . 1 6 . 1 DC H2' H 2.26 . 1 7 . 1 DC H2'' H 2.58 . 1 8 . 1 DC H3' H 4.57 . 1 9 . 1 DC H4' H 4.65 . 1 10 . 1 DC H5' H 4.01 . 2 11 . 1 DC H5'' H 4.05 . 2 12 . 1 DC P P -4.21 . 1 13 . 2 DG H1 H 13.33 . 1 14 . 2 DG H21 H 8.98 . 1 15 . 2 DG H22 H 6.47 . 1 16 . 2 DG H8 H 8.16 . 1 17 . 2 DG H1' H 6.20 . 1 18 . 2 DG H2' H 2.83 . 1 19 . 2 DG H2'' H 2.96 . 1 20 . 2 DG H3' H 5.04 . 1 21 . 2 DG H4' H 4.65 . 1 22 . 2 DG H5' H 4.07 . 2 23 . 2 DG H5'' H 4.23 . 2 24 . 2 DG P P -4.09 . 1 25 . 3 DC H41 H 8.67 . 1 26 . 3 DC H42 H 6.83 . 1 27 . 3 DC H6 H 7.65 . 1 28 . 3 DC H5 H 5.60 . 1 29 . 3 DC H1' H 6.48 . 1 30 . 3 DC H2' H 2.53 . 1 31 . 3 DC H2'' H 2.41 . 1 32 . 3 DC H3' H 5.11 . 1 33 . 3 DC H4' H 4.54 . 1 34 . 3 DC H5' H 4.30 . 2 35 . 3 DC H5'' H 4.37 . 2 36 . 3 DC P P -3.93 . 1 37 . 4 DT H3 H 10.76 . 1 38 . 4 DT H6 H 7.09 . 1 39 . 4 DT H71 H 1.73 . 1 40 . 4 DT H72 H 1.73 . 1 41 . 4 DT H73 H 1.73 . 1 42 . 4 DT H1' H 5.84 . 1 43 . 4 DT H2' H 1.84 . 1 44 . 4 DT H2'' H 2.37 . 1 45 . 4 DT H3' H 4.60 . 1 46 . 4 DT H4' H 3.36 . 1 47 . 4 DT H5' H 3.36 . 2 48 . 4 DT H5'' H 3.72 . 2 49 . 4 DT P P -3.97 . 1 50 . 5 DC H41 H 7.30 . 1 51 . 5 DC H42 H 6.77 . 1 52 . 5 DC H6 H 7.96 . 1 53 . 5 DC H5 H 6.11 . 1 54 . 5 DC H1' H 6.50 . 1 55 . 5 DC H2' H 2.35 . 1 56 . 5 DC H2'' H 2.59 . 1 57 . 5 DC H3' H 4.63 . 1 58 . 5 DC H4' H 4.63 . 1 59 . 5 DC H5' H 4.12 . 2 60 . 5 DC H5'' H 4.30 . 2 61 . 5 DC P P -4.18 . 1 62 . 6 DA H61 H 8.02 . 1 63 . 6 DA H62 H 6.93 . 1 64 . 6 DA H8 H 8.65 . 1 65 . 6 DA H2 H 8.53 . 1 66 . 6 DA H1' H 6.50 . 1 67 . 6 DA H2' H 2.92 . 1 68 . 6 DA H2'' H 3.18 . 1 69 . 6 DA H3' H 5.11 . 1 70 . 6 DA H4' H 4.69 . 1 71 . 6 DA H5' H 4.12 . 2 72 . 6 DA H5'' H 4.30 . 2 73 . 6 DA P P -4.06 . 1 74 . 7 DT H3 H 14.10 . 1 75 . 7 DT H6 H 7.53 . 1 76 . 7 DT H71 H 1.59 . 1 77 . 7 DT H72 H 1.59 . 1 78 . 7 DT H73 H 1.59 . 1 79 . 7 DT H1' H 6.52 . 1 80 . 7 DT H2' H 2.53 . 1 81 . 7 DT H2'' H 2.44 . 1 82 . 7 DT H3' H 5.14 . 1 83 . 7 DT H4' H 4.61 . 1 84 . 7 DT H5' H 4.38 . 2 85 . 7 DT H5'' H 4.38 . 2 86 . 7 DT P P -4.01 . 1 87 . 8 DT H3 H 10.87 . 1 88 . 8 DT H6 H 7.47 . 1 89 . 8 DT H71 H 1.86 . 1 90 . 8 DT H72 H 1.86 . 1 91 . 8 DT H73 H 1.86 . 1 92 . 8 DT H1' H 5.95 . 1 93 . 8 DT H2' H 1.93 . 1 94 . 8 DT H2'' H 2.42 . 1 95 . 8 DT H3' H 4.61 . 1 96 . 8 DT H4' H 3.22 . 1 97 . 8 DT H5' H 3.51 . 2 98 . 8 DT H5'' H 3.69 . 2 99 . 8 DT P P -3.75 . 1 stop_ save_