data_50246 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; [r(UGGUGGT)]4 G-quadruplex ; _BMRB_accession_number 50246 _BMRB_flat_file_name bmr50246.str _Entry_type original _Submission_date 2020-04-24 _Accession_date 2020-04-24 _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 Andralojc Witold . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 50 "31P chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-05-20 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 50242 '[r(UGGUGG)d(U)]4 G-quadruplex' 50244 "[r(UGGUGG)(2'OMeU)]4 G-quadruplex" 50245 '[r(UGGUGGC)]4 G-quadruplex' 50247 '[r(UGGUGG)d(T)]4 G-quadruplex' 50248 '[r(UGGUGG)(LNA-T)]4 G-quadruplex' 50249 '[r(UGGUGGPs)]4 G-quadruplex' stop_ _Original_release_date 2020-04-27 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; The origin of the high stability of 3'-terminal uridine tetrads. The contributions of hydrogen bonding, stacking interactions and steric factors evaluated using modified oligonucleotide analogs. ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Andralojc Witold . . 2 Pasternak Karol . . 3 Sarzynska Joanna . . 4 Zielinska Karolina . . 5 Kierzek Ryszard . . 6 Gdaniec Zofia . . stop_ _Journal_abbreviation 'Not known' _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 . _Details . save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name '[r(UGGUGGT)]4 G-quadruplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '[r(UGGUGGT)]4 G-quadruplex' $entity_1 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common entity_1 _Molecular_mass . _Mol_thiol_state 'not present' _Details 'X is 5-Methyluridine/ribothymidine' ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ; UGGUGGX ; loop_ _Residue_seq_code _Residue_label 1 U 2 G 3 G 4 U 5 G 6 G 7 38T stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_38T _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 5-methyluridine _BMRB_code 38T _PDB_code 38T _Standard_residue_derivative . _Molecular_mass 258.228 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OAC OAC O . 0 . ? CAM CAM C . 0 . ? NAI NAI N . 0 . ? CAL CAL C . 0 . ? OAB OAB O . 0 . ? CAK CAK C . 0 . ? CAA CAA C . 0 . ? CAG CAG C . 0 . ? NAR NAR N . 0 . ? C1' C1' C . 0 . ? O4' O4' O . 0 . ? C4' C4' C . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H3 H3 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 H . 0 . ? H14 H14 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 OAC CAM ? ? SING NAI CAM ? ? SING NAI CAL ? ? DOUB OAB CAL ? ? SING CAM NAR ? ? SING O2' C2' ? ? SING C2' C3' ? ? SING C2' C1' ? ? SING CAL CAK ? ? SING O3' C3' ? ? SING NAR C1' ? ? SING NAR CAG ? ? SING C3' C4' ? ? SING C1' O4' ? ? DOUB CAK CAG ? ? SING CAK CAA ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING O5' C5' ? ? SING NAI H1 ? ? SING CAA H2 ? ? SING CAA H3 ? ? SING CAA H4 ? ? SING CAG H5 ? ? SING C1' H6 ? ? SING C4' H7 ? ? SING C5' H8 ? ? SING C5' H9 ? ? SING O5' H10 ? ? SING C3' H11 ? ? SING O3' H12 ? ? SING C2' H13 ? ? SING O2' H14 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source_1 _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_1 _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 . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' 'sodium chloride' 150 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name TOPSPIN _Version . loop_ _Task collection stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Avance III' _Field_strength 700 _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-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-31H_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31H COSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _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' 150 . mM pH 6.8 . pH pressure 1 . atm temperature 298 . 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 TSP H 1 'methyl protons' ppm 0.00 internal direct . . . 1 TSP P 31 'methyl protons' ppm 0.00 internal indirect . . . . 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 'The protons of the 5-methyl group are marked as H7 in the CS file.' loop_ _Software_label $software_2 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-13C HSQC' '2D 1H-31H COSY' '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 '[r(UGGUGGT)]4 G-quadruplex' _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 U H1' H 5.335 0.01 1 2 1 1 U H2' H 3.843 0.01 1 3 1 1 U H3' H 4.553 0.01 1 4 1 1 U H4' H 4.315 0.01 1 5 1 1 U H5 H 5.717 0.01 1 6 1 1 U H5' H 4.045 0.01 2 7 1 1 U H5'' H 4.216 0.01 2 8 1 1 U H6 H 7.958 0.01 1 9 1 1 U P P -0.947 0.05 1 10 2 2 G H1' H 5.898 0.01 1 11 2 2 G H2' H 5.066 0.01 1 12 2 2 G H3' H 4.934 0.01 1 13 2 2 G H4' H 4.610 0.01 1 14 2 2 G H5' H 4.165 0.01 2 15 2 2 G H5'' H 4.374 0.01 2 16 2 2 G H8 H 8.304 0.01 1 17 2 2 G P P -5.007 0.05 1 18 3 3 G H1' H 6.247 0.01 1 19 3 3 G H2' H 4.862 0.01 1 20 3 3 G H3' H 4.368 0.01 1 21 3 3 G H4' H 4.728 0.01 1 22 3 3 G H5' H 4.372 0.01 2 23 3 3 G H5'' H 4.592 0.01 2 24 3 3 G H8 H 8.156 0.01 1 25 3 3 G P P -2.050 0.05 1 26 4 4 U H1' H 5.428 0.01 1 27 4 4 U H2' H 4.254 0.01 1 28 4 4 U H3' H 4.399 0.01 1 29 4 4 U H4' H 4.527 0.01 1 30 4 4 U H5 H 4.623 0.01 1 31 4 4 U H6 H 7.330 0.01 1 32 4 4 U P P -2.969 0.05 1 33 5 5 G H1' H 5.858 0.01 1 34 5 5 G H2' H 4.324 0.01 1 35 5 5 G H3' H 4.976 0.01 1 36 5 5 G H4' H 4.514 0.01 1 37 5 5 G H5' H 4.199 0.01 2 38 5 5 G H5'' H 4.709 0.01 2 39 5 5 G H8 H 8.427 0.01 1 40 5 5 G P P -5.074 0.05 1 41 6 6 G H1' H 6.172 0.01 1 42 6 6 G H2' H 4.369 0.01 1 43 6 6 G H3' H 4.747 0.01 1 44 6 6 G H4' H 4.481 0.01 1 45 6 6 G H5' H 4.151 0.01 2 46 6 6 G H5'' H 4.664 0.01 2 47 6 6 G H8 H 7.724 0.01 1 48 6 6 G P P -4.116 0.05 1 49 7 7 38T H1' H 5.728 0.01 1 50 7 7 38T H2' H 4.043 0.01 1 51 7 7 38T H3' H 4.225 0.01 1 52 7 7 38T H4' H 4.177 0.01 1 53 7 7 38T H5' H 4.058 0.01 2 54 7 7 38T H5'' H 4.240 0.01 2 55 7 7 38T H6 H 7.466 0.01 1 56 7 7 38T H7 H 1.578 0.01 1 57 7 7 38T P P -3.799 0.05 1 stop_ save_