data_34162 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of minimal i-motif domain ; _BMRB_accession_number 34162 _BMRB_flat_file_name bmr34162.str _Entry_type original _Submission_date 2017-07-12 _Accession_date 2017-11-22 _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 Mir B. . . 2 Serrano I. . . 3 Buitrago D. . . 4 Orozco M. . . 5 Escaja N. . . 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" 116 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-11-27 original BMRB . stop_ _Original_release_date 2017-11-22 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28933543 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Mir B. . . 2 Serrano I. . . 3 Buitrago D. . . 4 Orozco M. . . 5 Escaja N. . . 6 Gonzalez C. . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 139 _Journal_issue . _Journal_ASTM JACSAT _Journal_ISSN 1520-5126 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 13985 _Page_last 13988 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*TP*(DCP)P*GP*TP*TP*CP*(DCP)P*GP*TP*TP*TP*TP*TP*CP*GP*TP*TP*CP*CP*GP*T)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common entity_1 _Molecular_mass 6275.114 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; XCGTTCCGTTTTTCGTTCCG T ; loop_ _Residue_seq_code _Residue_label 1 THM 2 DNR 3 DG 4 DT 5 DT 6 DC 7 DNR 8 DG 9 DT 10 DT 11 DT 12 DT 13 DT 14 DC 15 DG 16 DT 17 DT 18 DC 19 DC 20 DG 21 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DNR _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common "2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE" _BMRB_code DNR _PDB_code DNR _Standard_residue_derivative . _Molecular_mass 308.205 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C1' C1' C . 0 . ? N1 N1 N . 0 . ? C6 C6 C . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 1 . ? C4 C4 C . 0 . ? N4 N4 N . 0 . ? C5 C5 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? OP3 OP3 O . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H1' H1' H . 0 . ? H6 H6 H . 0 . ? HN3 HN3 H . 0 . ? H41 H41 H . 0 . ? H42 H42 H . 0 . ? H5 H5 H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? HOP3 HOP3 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 P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C1' N1 ? ? SING C1' C2' ? ? SING C1' H1' ? ? SING N1 C6 ? ? SING N1 C2 ? ? DOUB C6 C5 ? ? SING C6 H6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? DOUB N3 C4 ? ? SING N3 HN3 ? ? SING C4 N4 ? ? SING C4 C5 ? ? SING N4 H41 ? ? SING N4 H42 ? ? SING C5 H5 ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C3' O3' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING OP3 HOP3 ? ? stop_ save_ save_chem_comp_THM _Saveframe_category polymer_residue _Mol_type 'DNA OH 5 PRIME TERMINUS' _Name_common THYMIDINE _BMRB_code THM _PDB_code THM _Standard_residue_derivative . _Molecular_mass 242.229 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? O2 O2 O . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? O4 O4 O . 0 . ? C5 C5 C . 0 . ? C5M C5M C . 0 . ? C6 C6 C . 0 . ? HO5' HO5' H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2'1 H2'1 H . 0 . ? H2'2 H2'2 H . 0 . ? H1' H1' H . 0 . ? HN3 HN3 H . 0 . ? HM51 HM51 H . 0 . ? HM52 HM52 H . 0 . ? HM53 HM53 H . 0 . ? H6 H6 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 SING O5' C5' ? ? SING O5' HO5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2'1 ? ? SING C2' H2'2 ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 HN3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C5M ? ? DOUB C5 C6 ? ? SING C5M HM51 ? ? SING C5M HM52 ? ? SING C5M HM53 ? ? SING C6 H6 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity_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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.5 mM LL3, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM 'natural abundance' NaPi 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version . loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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 'ionic strength' 10 . mM pH 7.0 . pH pressure 1 . atm temperature 278 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _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 0.000 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H TOCSY' '2D DQF-COSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 1 THM H1' H 6.47 0.00 1 2 1 1 THM H2'1 H 2.35 0.01 . 3 1 1 THM H2'2 H 2.53 0.00 . 4 1 1 THM H6 H 7.84 0.00 1 5 1 1 THM HM51 H 1.93 0.00 1 6 1 1 THM HM52 H 1.93 0.00 1 7 1 1 THM HM53 H 1.93 0.00 1 8 1 1 THM HN3 H 11.40 0.00 1 9 2 2 DNR H1' H 6.32 0.00 1 10 2 2 DNR H2' H 1.06 0.00 . 11 2 2 DNR H2'' H 2.26 0.00 . 12 2 2 DNR H5 H 6.11 0.01 1 13 2 2 DNR H6 H 7.44 0.00 1 14 2 2 DNR H41 H 7.28 0.00 . 15 2 2 DNR H42 H 8.62 0.00 . 16 3 3 DG H1 H 10.26 0.01 1 17 3 3 DG H1' H 5.94 0.01 1 18 3 3 DG H2' H 2.93 0.00 . 19 3 3 DG H2'' H 2.66 0.01 . 20 3 3 DG H8 H 8.31 0.00 1 21 3 3 DG H21 H 5.84 0.00 . 22 3 3 DG H22 H 8.60 0.00 . 23 4 4 DT H1' H 6.13 0.00 1 24 4 4 DT H6 H 7.62 0.00 1 25 4 4 DT H71 H 1.75 0.01 1 26 4 4 DT H72 H 1.75 0.01 1 27 4 4 DT H73 H 1.75 0.01 1 28 6 6 DC H1' H 6.30 0.01 1 29 6 6 DC H2' H 2.44 0.00 . 30 6 6 DC H2'' H 2.44 0.00 . 31 6 6 DC H5 H 6.13 0.00 1 32 6 6 DC H6 H 7.93 0.01 1 33 6 6 DC H41 H 7.46 0.01 . 34 6 6 DC H42 H 8.59 0.01 . 35 7 7 DNR H1' H 6.27 0.01 1 36 7 7 DNR H2' H 0.78 0.01 . 37 7 7 DNR H2'' H 2.09 0.00 . 38 7 7 DNR H5 H 5.95 0.01 1 39 7 7 DNR H6 H 7.45 0.00 1 40 7 7 DNR H41 H 8.19 0.00 . 41 7 7 DNR H42 H 10.66 0.00 . 42 8 8 DG H1 H 13.94 0.00 1 43 8 8 DG H1' H 6.03 0.01 1 44 8 8 DG H2' H 3.06 0.00 . 45 8 8 DG H2'' H 2.69 0.01 . 46 8 8 DG H8 H 8.32 0.00 1 47 8 8 DG H21 H 7.63 0.01 . 48 8 8 DG H22 H 8.20 0.00 . 49 9 9 DT H1' H 5.93 0.00 1 50 9 9 DT H6 H 7.63 0.00 1 51 9 9 DT H71 H 1.69 0.00 1 52 9 9 DT H72 H 1.69 0.00 1 53 9 9 DT H73 H 1.69 0.00 1 54 10 10 DT H1' H 5.54 0.00 1 55 10 10 DT H6 H 7.76 0.00 1 56 11 11 DT H71 H 1.99 0.00 1 57 11 11 DT H72 H 1.99 0.00 1 58 11 11 DT H73 H 1.99 0.00 1 59 12 12 DT H6 H 7.84 0.00 1 60 12 12 DT H71 H 1.99 0.00 1 61 12 12 DT H72 H 1.99 0.00 1 62 12 12 DT H73 H 1.99 0.00 1 63 13 13 DT H1' H 6.12 0.01 1 64 13 13 DT H2' H 2.46 0.00 . 65 13 13 DT H2'' H 2.63 0.01 . 66 13 13 DT H3 H 11.20 0.00 1 67 13 13 DT H6 H 7.74 0.00 1 68 13 13 DT H71 H 1.71 0.00 1 69 13 13 DT H72 H 1.71 0.00 1 70 13 13 DT H73 H 1.71 0.00 1 71 14 14 DC H1' H 6.41 0.00 1 72 14 14 DC H2' H 1.07 0.00 . 73 14 14 DC H2'' H 2.17 0.00 . 74 14 14 DC H5 H 6.39 0.02 1 75 14 14 DC H6 H 7.49 0.00 1 76 14 14 DC H41 H 6.97 0.00 . 77 14 14 DC H42 H 8.66 0.01 . 78 15 15 DG H1' H 5.99 0.00 1 79 15 15 DG H2' H 2.99 0.00 . 80 15 15 DG H2'' H 2.70 0.00 . 81 15 15 DG H8 H 8.39 0.00 1 82 15 15 DG H21 H 5.30 0.01 . 83 15 15 DG H22 H 9.07 0.01 . 84 16 16 DT H1' H 6.00 0.00 1 85 16 16 DT H6 H 7.64 0.00 1 86 16 16 DT H71 H 1.81 0.01 1 87 16 16 DT H72 H 1.81 0.01 1 88 16 16 DT H73 H 1.81 0.01 1 89 18 18 DC H1' H 6.30 0.00 1 90 18 18 DC H2' H 2.44 0.00 . 91 18 18 DC H2'' H 2.44 0.00 . 92 18 18 DC H5 H 6.13 0.00 1 93 18 18 DC H6 H 7.93 0.01 1 94 18 18 DC H41 H 7.43 0.00 . 95 18 18 DC H42 H 8.55 0.00 . 96 19 19 DC H1' H 6.23 0.01 1 97 19 19 DC H2' H 0.76 0.00 . 98 19 19 DC H2'' H 2.02 0.00 . 99 19 19 DC H3' H 4.70 0.00 1 100 19 19 DC H4' H 4.50 0.00 1 101 19 19 DC H5 H 5.95 0.01 1 102 19 19 DC H6 H 7.41 0.00 1 103 19 19 DC H41 H 8.05 0.00 . 104 19 19 DC H42 H 10.62 0.01 . 105 20 20 DG H1 H 13.65 0.00 1 106 20 20 DG H1' H 5.98 0.01 1 107 20 20 DG H2' H 3.04 0.00 . 108 20 20 DG H2'' H 2.66 0.00 . 109 20 20 DG H8 H 8.27 0.00 1 110 20 20 DG H21 H 7.67 0.01 . 111 20 20 DG H22 H 7.96 0.00 . 112 21 21 DT H1' H 5.96 0.01 1 113 21 21 DT H6 H 7.63 0.00 1 114 21 21 DT H71 H 1.73 0.01 1 115 21 21 DT H72 H 1.73 0.01 1 116 21 21 DT H73 H 1.73 0.01 1 stop_ save_