data_25099 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Dimeric structure of the Human A-box ; _BMRB_accession_number 25099 _BMRB_flat_file_name bmr25099.str _Entry_type original _Submission_date 2014-07-18 _Accession_date 2014-07-18 _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 Garavis Miguel . . 2 Escaja Nuria . . 3 Gabelica Valerie . . 4 Villasante Alfredo . . 5 Gonzalez Carlos . . 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 2015-06-01 original BMRB . stop_ _Original_release_date 2015-06-01 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26013031 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Garavis Miguel . . 2 Escaja Nuria . . 3 Gabelica Valerie . . 4 Villasante Alfredo . . 5 Gonzalez Carlos . . stop_ _Journal_abbreviation Chemistry _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Hs2 dimer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "DNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3')_1" $DNA_(5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') "DNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3')_2" $DNA_(5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_(5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_(5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') _Molecular_mass 2945.966 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; TCCTTTTCCA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DC 3 3 DC 4 4 DT 5 5 DT 6 6 DT 7 7 DT 8 8 DC 9 9 DC 10 10 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 $DNA_(5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') Human 9606 Eukaryota Metazoa Homo sapiens 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_(5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') 'obtained from a vendor' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_Hs2 _Saveframe_category sample _Sample_type solution _Details 'Buffer pH = 4.0' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling 'sodium phosphate' 25 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' $DNA_(5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') 2 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _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_ ######################### # 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_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $Hs2 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $Hs2 save_ save_2D_1H-1H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $Hs2 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' 125 . mM pH 4 . pH pressure 1 . atm temperature 273 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_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 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' stop_ loop_ _Sample_label $Hs2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name "DNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3')_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 DT H1' H 5.43 0.01 1 2 1 1 DT H2' H 2.51 0.01 1 3 1 1 DT H2'' H 1.99 0.01 1 4 1 1 DT H3' H 4.63 0.01 1 5 1 1 DT H4' H 3.77 0.01 1 6 1 1 DT H5' H 3.66 0.01 2 7 1 1 DT H5'' H 3.66 0.01 2 8 1 1 DT H6 H 7.77 0.01 1 9 1 1 DT H71 H 1.74 0.01 1 10 1 1 DT H72 H 1.74 0.01 1 11 1 1 DT H73 H 1.74 0.01 1 12 2 2 DC H1' H 6.56 0.01 1 13 2 2 DC H2' H 2.13 0.01 1 14 2 2 DC H2'' H 2.61 0.01 1 15 2 2 DC H3' H 4.85 0.01 1 16 2 2 DC H4' H 4.20 0.01 1 17 2 2 DC H5 H 5.88 0.01 1 18 2 2 DC H6 H 7.93 0.01 1 19 2 2 DC H41 H 8.56 0.01 1 20 2 2 DC H42 H 9.95 0.01 1 21 3 3 DC H1' H 6.43 0.01 1 22 3 3 DC H2' H 2.61 0.01 1 23 3 3 DC H2'' H 2.61 0.01 1 24 3 3 DC H3' H 4.89 0.01 1 25 3 3 DC H4' H 4.42 0.01 1 26 3 3 DC H5 H 6.01 0.01 1 27 3 3 DC H6 H 7.91 0.01 1 28 3 3 DC H41 H 8.31 0.01 1 29 3 3 DC H42 H 9.50 0.01 1 30 4 4 DT H1' H 6.45 0.01 1 31 4 4 DT H2' H 2.35 0.01 1 32 4 4 DT H2'' H 2.55 0.01 1 33 4 4 DT H3' H 4.60 0.01 1 34 4 4 DT H4' H 4.54 0.01 1 35 4 4 DT H5' H 4.17 0.01 2 36 4 4 DT H5'' H 3.95 0.01 2 37 4 4 DT H6 H 7.78 0.01 1 38 4 4 DT H71 H 1.92 0.01 1 39 4 4 DT H72 H 1.92 0.01 1 40 4 4 DT H73 H 1.92 0.01 1 41 5 5 DT H1' H 6.36 0.01 1 42 5 5 DT H2' H 2.26 0.01 1 43 5 5 DT H2'' H 2.77 0.01 1 44 5 5 DT H3' H 4.75 0.01 1 45 5 5 DT H4' H 4.50 0.01 1 46 5 5 DT H5' H 4.16 0.01 2 47 5 5 DT H5'' H 4.50 0.01 2 48 5 5 DT H6 H 7.77 0.01 1 49 5 5 DT H71 H 1.95 0.01 1 50 5 5 DT H72 H 1.95 0.01 1 51 5 5 DT H73 H 1.95 0.01 1 52 6 6 DT H1' H 6.04 0.01 1 53 6 6 DT H2' H 2.07 0.01 1 54 6 6 DT H2'' H 2.33 0.01 1 55 6 6 DT H3' H 4.84 0.01 1 56 6 6 DT H4' H 3.73 0.01 1 57 6 6 DT H5' H 3.96 0.01 2 58 6 6 DT H5'' H 3.93 0.01 2 59 6 6 DT H6 H 7.63 0.01 1 60 6 6 DT H71 H 1.91 0.01 1 61 6 6 DT H72 H 1.91 0.01 1 62 6 6 DT H73 H 1.91 0.01 1 63 7 7 DT H1' H 6.35 0.01 1 64 7 7 DT H2' H 2.60 0.01 1 65 7 7 DT H2'' H 2.16 0.01 1 66 7 7 DT H3' H 4.89 0.01 1 67 7 7 DT H4' H 4.33 0.01 1 68 7 7 DT H6 H 7.83 0.01 1 69 7 7 DT H71 H 1.89 0.01 1 70 7 7 DT H72 H 1.89 0.01 1 71 7 7 DT H73 H 1.89 0.01 1 72 8 8 DC H1' H 6.44 0.01 1 73 8 8 DC H2' H 2.01 0.01 1 74 8 8 DC H2'' H 2.54 0.01 1 75 8 8 DC H3' H 4.71 0.01 1 76 8 8 DC H4' H 4.09 0.01 1 77 8 8 DC H5 H 5.92 0.01 1 78 8 8 DC H6 H 7.74 0.01 1 79 8 8 DC H41 H 8.15 0.01 1 80 8 8 DC H42 H 8.92 0.01 1 81 9 9 DC H1' H 6.14 0.01 1 82 9 9 DC H2' H 2.17 0.01 1 83 9 9 DC H2'' H 2.54 0.01 1 84 9 9 DC H3' H 4.61 0.01 1 85 9 9 DC H4' H 4.25 0.01 1 86 9 9 DC H5 H 6.00 0.01 1 87 9 9 DC H5' H 4.14 0.01 2 88 9 9 DC H5'' H 3.96 0.01 2 89 9 9 DC H6 H 7.74 0.01 1 90 9 9 DC H41 H 8.23 0.01 1 91 9 9 DC H42 H 9.03 0.01 1 92 10 10 DA H1' H 6.52 0.01 1 93 10 10 DA H2 H 8.50 0.01 1 94 10 10 DA H2' H 2.67 0.01 1 95 10 10 DA H2'' H 2.97 0.01 1 96 10 10 DA H3' H 4.71 0.01 1 97 10 10 DA H4' H 4.29 0.01 1 98 10 10 DA H5' H 4.01 0.01 2 99 10 10 DA H5'' H 4.01 0.01 2 100 10 10 DA H8 H 8.45 0.01 1 stop_ save_