data_18950 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; THE SOLUTION STRUCTURE OF 3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX ; _BMRB_accession_number 18950 _BMRB_flat_file_name bmr18950.str _Entry_type original _Submission_date 2013-01-15 _Accession_date 2013-01-15 _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 Plevnik Miha . . 2 Cevec Mirko . . 3 Plavec Janez . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 173 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-11-26 original author . stop_ _Original_release_date 2013-11-26 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR structure of 2'-O-(2-methoxyethyl) modified and C5-methylated RNA dodecamer duplex.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24012551 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Plevnik Miha . . 2 Cevec Mirko . . 3 Plavec Janez . . stop_ _Journal_abbreviation Biochimie _Journal_volume 95 _Journal_issue 12 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2385 _Page_last 2391 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name '3',5'-LINKED 2'-O-(2-METHOXYETHYL)-RNA DUPLEX' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA (5'-R(P*(G48)P*(A44)P*(A44)P*(T39)P*(T39))-3')_1' $5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' 'RNA (5'-R(P*(G48)P*(A44)P*(A44)P*(T39)P*(T39))-3')_2' $5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-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_5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' _Molecular_mass 1889.457 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence XXXXXXXXXXXG loop_ _Residue_seq_code _Residue_label 1 C5L 2 G48 3 C5L 4 G48 5 A44 6 A44 7 T39 8 T39 9 C5L 10 G48 11 C5L 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_C5L _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common '2'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate)' _BMRB_code C5L _PDB_code C5L _Standard_residue_derivative . _Molecular_mass 395.302 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? CA' CA' C . 0 . ? CB' CB' C . 0 . ? CD' CD' C . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? H5'A H5'A H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H7A H7A H . 0 . ? H7B H7B H . 0 . ? HA' HA' H . 0 . ? HA'A HA'A H . 0 . ? HB' HB' H . 0 . ? HB'A HB'A H . 0 . ? HD' HD' H . 0 . ? HD'A HD'A H . 0 . ? HD'B HD'B H . 0 . ? HN4 HN4 H . 0 . ? HN4A HN4A H . 0 . ? HO3' HO3' H . 0 . ? HOP1 HOP1 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? N4 N4 N . 0 . ? O2 O2 O . 0 . ? O2' O2' O . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? OC' OC' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 OP2 P ? ? SING O5' P ? ? SING P OP3 ? ? SING P OP1 ? ? SING C2 N1 ? ? SING C6 N1 ? ? SING N1 C1' ? ? SING N3 C2 ? ? DOUB C2 O2 ? ? DOUB C4 N3 ? ? SING N4 C4 ? ? SING C4 C5 ? ? SING HN4 N4 ? ? SING HN4A N4 ? ? SING C7 C5 ? ? DOUB C5 C6 ? ? SING C6 H6 ? ? SING H7A C7 ? ? SING H7B C7 ? ? SING C7 H7 ? ? SING H1' C1' ? ? SING C1' C2' ? ? SING C1' O4' ? ? SING H2' C2' ? ? SING C2' O2' ? ? SING C2' C3' ? ? SING CA' O2' ? ? SING H3' C3' ? ? SING C3' C4' ? ? SING C3' O3' ? ? SING O3' HO3' ? ? SING O4' C4' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING O5' C5' ? ? SING C5' H5' ? ? SING C5' H5'A ? ? SING HA' CA' ? ? SING HA'A CA' ? ? SING CA' CB' ? ? SING OC' CB' ? ? SING CB' HB'A ? ? SING CB' HB' ? ? SING CD' OC' ? ? SING HD' CD' ? ? SING HD'A CD' ? ? SING CD' HD'B ? ? SING OP1 HOP1 ? ? SING OP3 HOP3 ? ? stop_ save_ save_chem_comp_G48 _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common 2'-O-METHYOXYETHYL-GUANOSINE-5'-MONOPHOSPHATE _BMRB_code G48 _PDB_code G48 _Standard_residue_derivative . _Molecular_mass 421.300 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C6 C6 C . 0 . ? C8 C8 C . 0 . ? CA' CA' C . 0 . ? CB' CB' C . 0 . ? CD' CD' C . 0 . ? H1 H1 H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H8 H8 H . 0 . ? HCA1 HCA1 H . 0 . ? HCA2 HCA2 H . 0 . ? HCB1 HCB1 H . 0 . ? HCB2 HCB2 H . 0 . ? HCD1 HCD1 H . 0 . ? HCD2 HCD2 H . 0 . ? HCD3 HCD3 H . 0 . ? HO3' HO3' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? N7 N7 N . 0 . ? N9 N9 N . 0 . ? O2' O2' O . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? O6 O6 O . 0 . ? OC' OC' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 OP1 P ? ? SING P O5' ? ? SING P OP3 ? ? SING C5' O5' ? ? SING C5' C4' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING O4' C1' ? ? SING O3' C3' ? ? SING C3' C2' ? ? SING C1' C2' ? ? SING C1' N9 ? ? SING O2' C2' ? ? SING O2' CA' ? ? SING CD' OC' ? ? SING C8 N9 ? ? DOUB C8 N7 ? ? SING CB' OC' ? ? SING CB' CA' ? ? SING N9 C4 ? ? SING N7 C5 ? ? DOUB C4 C5 ? ? SING C4 N3 ? ? SING C5 C6 ? ? DOUB N3 C2 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING C2 N1 ? ? SING C2 N2 ? ? SING P OP2 ? ? SING OP3 HOP3 ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' H4' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' H2' ? ? SING C1' H1' ? ? SING C8 H8 ? ? SING N1 H1 ? ? SING N2 H21 ? ? SING N2 H22 ? ? SING CA' HCA2 ? ? SING CA' HCA1 ? ? SING CB' HCB1 ? ? SING CB' HCB2 ? ? SING CD' HCD1 ? ? SING CD' HCD2 ? ? SING CD' HCD3 ? ? SING OP2 HOP2 ? ? stop_ save_ save_chem_comp_A44 _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common '2'-O-METHYOXYETHYL-ADENOSINE 5'-MONOPHOSPHATE' _BMRB_code A44 _PDB_code A44 _Standard_residue_derivative . _Molecular_mass 405.300 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C6 C6 C . 0 . ? C8 C8 C . 0 . ? CA' CA' C . 0 . ? CB' CB' C . 0 . ? CD' CD' C . 0 . ? H1' H1' H . 0 . ? H2 H2 H . 0 . ? H2' H2' H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H8 H8 H . 0 . ? HCA1 HCA1 H . 0 . ? HCA2 HCA2 H . 0 . ? HCB1 HCB1 H . 0 . ? HCB2 HCB2 H . 0 . ? HCD1 HCD1 H . 0 . ? HCD2 HCD2 H . 0 . ? HCD3 HCD3 H . 0 . ? HO3' HO3' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? N6 N6 N . 0 . ? N7 N7 N . 0 . ? N9 N9 N . 0 . ? O2' O2' O . 0 . ? O3' O3' O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? OC' OC' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 C2 N1 ? ? SING C2 N3 ? ? SING N1 C6 ? ? SING CB' CA' ? ? SING CB' OC' ? ? DOUB N3 C4 ? ? SING C6 N6 ? ? DOUB C6 C5 ? ? SING CD' OC' ? ? SING CA' O2' ? ? SING C4 C5 ? ? SING C4 N9 ? ? SING C5 N7 ? ? SING O2' C2' ? ? SING C2' C1' ? ? SING C2' C3' ? ? SING N9 C1' ? ? SING N9 C8 ? ? DOUB N7 C8 ? ? SING C1' O4' ? ? SING O3' C3' ? ? SING C3' C4' ? ? SING O4' C4' ? ? SING C4' C5' ? ? SING O5' C5' ? ? SING O5' P ? ? DOUB OP1 P ? ? SING P OP2 ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' H4' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' H2' ? ? SING C1' H1' ? ? SING C8 H8 ? ? SING N6 H61 ? ? SING N6 H62 ? ? SING C2 H2 ? ? SING CA' HCA2 ? ? SING CA' HCA1 ? ? SING CD' HCD1 ? ? SING CD' HCD2 ? ? SING CD' HCD3 ? ? SING CB' HCB1 ? ? SING CB' HCB2 ? ? SING OP3 HOP3 ? ? stop_ save_ save_chem_comp_T39 _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common '2'-O-METHOXYETHYLENE THYMIDINE 5'-MONOPHOSPHATE' _BMRB_code T39 _PDB_code T39 _Standard_residue_derivative . _Molecular_mass 396.287 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1' C1' C . 0 . ? C2 C2 C . 0 . ? C2' C2' C . 0 . ? C3' C3' C . 0 . ? C4 C4 C . 0 . ? C4' C4' C . 0 . ? C5 C5 C . 0 . ? C5' C5' C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? CA' CA' C . 0 . ? CB' CB' C . 0 . ? CD' CD' C . 0 . ? H1' H1' H . 0 . ? H3 H3 H . 0 . ? H3' H3' H . 0 . ? H4' H4' H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H71 H71 H . 0 . ? H72 H72 H . 0 . ? H73 H73 H . 0 . ? HCA1 HCA1 H . 0 . ? HCA2 HCA2 H . 0 . ? HCB1 HCB1 H . 0 . ? HCB2 HCB2 H . 0 . ? HCD1 HCD1 H . 0 . ? HCD2 HCD2 H . 0 . ? HCD3 HCD3 H . 0 . ? HO3' HO3' H . 0 . ? HOP2 HOP2 H . 0 . ? HOP3 HOP3 H . 0 . ? N1 N1 N . 0 . ? N3 N3 N . 0 . ? O2 O2 O . 0 . ? O2' O2' O . 0 . ? O3' O3' O . 0 . ? O4 O4 O . 0 . ? O4' O4' O . 0 . ? O5' O5' O . 0 . ? OC' OC' O . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? P P P . 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 CD' OC' ? ? SING OC' CB' ? ? SING CB' CA' ? ? SING CA' O2' ? ? SING O2' C2' ? ? SING O3' C3' ? ? SING C2' C3' ? ? SING C2' C1' ? ? SING C3' C4' ? ? DOUB O2 C2 ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C1' O4' ? ? SING C1' N1 ? ? SING C2 N1 ? ? SING C2 N3 ? ? SING N1 C6 ? ? SING C5' O5' ? ? SING N3 C4 ? ? SING O5' P ? ? DOUB C6 C5 ? ? SING C4 C5 ? ? DOUB C4 O4 ? ? SING C5 C7 ? ? DOUB OP1 P ? ? SING P OP2 ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' H4' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' H7 ? ? SING C1' H1' ? ? SING N3 H3 ? ? SING C7 H71 ? ? SING C7 H72 ? ? SING C7 H73 ? ? SING C6 H6 ? ? SING CA' HCA2 ? ? SING CA' HCA1 ? ? SING CD' HCD1 ? ? SING CD' HCD2 ? ? SING CD' HCD3 ? ? SING CB' HCB1 ? ? SING CB' HCB2 ? ? SING OP3 HOP3 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' . . . . . . 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 _Details $5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' 'chemical synthesis' . . . . . 'SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE' 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 $5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' 2.5 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $5'-R(*(C5L)P*(G48)P*(C5L)P*(G48)P*(A44)P*(A44)P*(T39)P*(T39)P*(C5L)P*(G48)P*(C5L))-D(P*(DG))-3' 2.5 mM 'natural abundance' 'potassium chloride' 100 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6.1B loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version 2000 loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task processing stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 7 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Unity Inova' _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_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_2 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 303 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 100 . mM stop_ save_ save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 278 . K pH 7.0 . pH pressure 1 . atm 'ionic strength' 100 . mM 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 external direct . . . 1 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(P*(G48)P*(A44)P*(A44)P*(T39)P*(T39))-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 C5L H1' H 5.767 0.02 1 2 1 1 C5L H2' H 4.443 0.02 1 3 1 1 C5L H3' H 4.634 0.02 1 4 1 1 C5L H41 H 8.403 0.02 1 5 1 1 C5L H42 H 6.665 0.02 1 6 1 1 C5L H6 H 7.994 0.02 1 7 1 1 C5L H7* H 1.917 0.02 1 8 1 1 C5L HCA* H 4.108 0.02 1 9 1 1 C5L HCD* H 3.433 0.02 1 10 2 2 G48 H1 H 12.877 0.02 1 11 2 2 G48 H1' H 6.023 0.02 1 12 2 2 G48 H2' H 4.463 0.02 1 13 2 2 G48 H3' H 4.628 0.02 1 14 2 2 G48 H8 H 7.650 0.02 1 15 2 2 G48 HCA* H 4.349 0.02 1 16 2 2 G48 HCD* H 3.489 0.02 1 17 3 3 C5L H1' H 5.701 0.02 1 18 3 3 C5L H2' H 4.477 0.02 1 19 3 3 C5L H3' H 4.569 0.02 1 20 3 3 C5L H41 H 8.786 0.02 1 21 3 3 C5L H42 H 6.255 0.02 1 22 3 3 C5L H6 H 7.615 0.02 1 23 3 3 C5L H7* H 1.385 0.02 1 24 3 3 C5L HCA* H 4.085 0.02 1 25 3 3 C5L HCD* H 3.474 0.02 1 26 4 4 G48 H1 H 11.937 0.02 1 27 4 4 G48 H1' H 5.920 0.02 1 28 4 4 G48 H2' H 4.477 0.02 1 29 4 4 G48 H3' H 4.570 0.02 1 30 4 4 G48 H8 H 7.466 0.02 1 31 4 4 G48 HCA* H 4.278 0.02 1 32 4 4 G48 HCD* H 3.496 0.02 1 33 5 5 A44 H1' H 6.069 0.02 1 34 5 5 A44 H2 H 7.202 0.02 1 35 5 5 A44 H2' H 4.563 0.02 1 36 5 5 A44 H3' H 4.681 0.02 1 37 5 5 A44 H61 H 7.949 0.02 1 38 5 5 A44 H62 H 6.724 0.02 1 39 5 5 A44 H8 H 7.662 0.02 1 40 5 5 A44 HCA* H 4.203 0.02 1 41 5 5 A44 HCD* H 3.472 0.02 1 42 6 6 A44 H1' H 6.183 0.02 1 43 6 6 A44 H2 H 7.791 0.02 1 44 6 6 A44 H2' H 4.449 0.02 1 45 6 6 A44 H3' H 4.327 0.02 1 46 6 6 A44 H61 H 8.382 0.02 1 47 6 6 A44 H62 H 6.752 0.02 1 48 6 6 A44 H8 H 7.386 0.02 1 49 6 6 A44 HCA* H 4.316 0.02 1 50 6 6 A44 HCD* H 3.506 0.02 1 51 7 7 T39 H1' H 5.871 0.02 1 52 7 7 T39 H3 H 13.900 0.02 1 53 7 7 T39 H3' H 4.400 0.02 1 54 7 7 T39 H6 H 7.310 0.02 1 55 7 7 T39 H7 H 4.225 0.02 1 56 7 7 T39 H7* H 1.078 0.02 1 57 8 8 T39 H1' H 5.940 0.02 1 58 8 8 T39 H3 H 13.484 0.02 1 59 8 8 T39 H3' H 4.505 0.02 1 60 8 8 T39 H6 H 7.849 0.02 1 61 8 8 T39 H7 H 4.252 0.02 1 62 8 8 T39 H7* H 1.476 0.02 1 63 8 8 T39 HCA* H 4.188 0.02 1 64 9 9 C5L H1' H 5.695 0.02 1 65 9 9 C5L H2' H 4.269 0.02 1 66 9 9 C5L H3' H 4.581 0.02 1 67 9 9 C5L H41 H 8.635 0.02 1 68 9 9 C5L H42 H 6.433 0.02 1 69 9 9 C5L H6 H 7.793 0.02 1 70 9 9 C5L H7* H 1.610 0.02 1 71 9 9 C5L HCA* H 4.110 0.02 1 72 10 10 G48 H1 H 12.679 0.02 1 73 10 10 G48 H1' H 5.831 0.02 1 74 10 10 G48 H2' H 4.327 0.02 1 75 10 10 G48 H3' H 4.539 0.02 1 76 10 10 G48 H8 H 7.410 0.02 1 77 10 10 G48 HCA* H 4.268 0.02 1 78 10 10 G48 HCD* H 3.473 0.02 1 79 11 11 C5L H1' H 5.661 0.02 1 80 11 11 C5L H2' H 4.180 0.02 1 81 11 11 C5L H41 H 8.815 0.02 1 82 11 11 C5L H42 H 6.266 0.02 1 83 11 11 C5L H6 H 7.553 0.02 1 84 11 11 C5L H7* H 1.317 0.02 1 85 11 11 C5L HCD* H 3.503 0.02 1 86 12 12 DG H1' H 6.079 0.02 1 87 12 12 DG H8 H 7.543 0.02 1 stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_2 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'RNA (5'-R(P*(G48)P*(A44)P*(A44)P*(T39)P*(T39))-3')_2' _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 13 1 C5L H1' H 5.767 0.02 1 2 13 1 C5L H2' H 4.443 0.02 1 3 13 1 C5L H3' H 4.634 0.02 1 4 13 1 C5L H41 H 8.403 0.02 1 5 13 1 C5L H42 H 6.665 0.02 1 6 13 1 C5L H6 H 7.994 0.02 1 7 13 1 C5L H7* H 1.917 0.02 1 8 13 1 C5L HCA* H 4.108 0.02 1 9 13 1 C5L HCD* H 3.433 0.02 1 10 14 2 G48 H1 H 12.877 0.02 1 11 14 2 G48 H1' H 6.023 0.02 1 12 14 2 G48 H2' H 4.463 0.02 1 13 14 2 G48 H3' H 4.628 0.02 1 14 14 2 G48 H8 H 7.650 0.02 1 15 14 2 G48 HCA* H 4.349 0.02 1 16 14 2 G48 HCD* H 3.489 0.02 1 17 15 3 C5L H1' H 5.701 0.02 1 18 15 3 C5L H2' H 4.477 0.02 1 19 15 3 C5L H3' H 4.569 0.02 1 20 15 3 C5L H41 H 8.786 0.02 1 21 15 3 C5L H42 H 6.255 0.02 1 22 15 3 C5L H6 H 7.615 0.02 1 23 15 3 C5L H7* H 1.385 0.02 1 24 15 3 C5L HCA* H 4.085 0.02 1 25 15 3 C5L HCD* H 3.474 0.02 1 26 16 4 G48 H1 H 11.937 0.02 1 27 16 4 G48 H1' H 5.920 0.02 1 28 16 4 G48 H2' H 4.477 0.02 1 29 16 4 G48 H3' H 4.570 0.02 1 30 16 4 G48 H8 H 7.466 0.02 1 31 16 4 G48 HCA* H 4.278 0.02 1 32 16 4 G48 HCD* H 3.496 0.02 1 33 17 5 A44 H1' H 6.069 0.02 1 34 17 5 A44 H2 H 7.202 0.02 1 35 17 5 A44 H2' H 4.563 0.02 1 36 17 5 A44 H3' H 4.681 0.02 1 37 17 5 A44 H61 H 7.949 0.02 1 38 17 5 A44 H62 H 6.724 0.02 1 39 17 5 A44 H8 H 7.662 0.02 1 40 17 5 A44 HCA* H 4.203 0.02 1 41 17 5 A44 HCD* H 3.472 0.02 1 42 18 6 A44 H1' H 6.183 0.02 1 43 18 6 A44 H2 H 7.791 0.02 1 44 18 6 A44 H2' H 4.449 0.02 1 45 18 6 A44 H3' H 4.327 0.02 1 46 18 6 A44 H61 H 8.382 0.02 1 47 18 6 A44 H62 H 6.752 0.02 1 48 18 6 A44 H8 H 7.386 0.02 1 49 18 6 A44 HCA* H 4.316 0.02 1 50 18 6 A44 HCD* H 3.506 0.02 1 51 19 7 T39 H1' H 5.871 0.02 1 52 19 7 T39 H2' H 4.225 0.02 1 53 19 7 T39 H3 H 13.900 0.02 1 54 19 7 T39 H3' H 4.400 0.02 1 55 19 7 T39 H6 H 7.310 0.02 1 56 19 7 T39 H7* H 1.078 0.02 1 57 20 8 T39 H1' H 5.940 0.02 1 58 20 8 T39 H2' H 4.252 0.02 1 59 20 8 T39 H3 H 13.484 0.02 1 60 20 8 T39 H3' H 4.505 0.02 1 61 20 8 T39 H6 H 7.849 0.02 1 62 20 8 T39 H7* H 1.476 0.02 1 63 20 8 T39 HCA* H 4.188 0.02 1 64 21 9 C5L H1' H 5.695 0.02 1 65 21 9 C5L H2' H 4.269 0.02 1 66 21 9 C5L H3' H 4.581 0.02 1 67 21 9 C5L H41 H 8.635 0.02 1 68 21 9 C5L H42 H 6.433 0.02 1 69 21 9 C5L H6 H 7.793 0.02 1 70 21 9 C5L H7* H 1.610 0.02 1 71 21 9 C5L HCA* H 4.110 0.02 1 72 22 10 G48 H1 H 12.679 0.02 1 73 22 10 G48 H1' H 5.831 0.02 1 74 22 10 G48 H2' H 4.327 0.02 1 75 22 10 G48 H3' H 4.539 0.02 1 76 22 10 G48 H8 H 7.410 0.02 1 77 22 10 G48 HCA* H 4.268 0.02 1 78 22 10 G48 HCD* H 3.473 0.02 1 79 23 11 C5L H1' H 5.661 0.02 1 80 23 11 C5L H2' H 4.180 0.02 1 81 23 11 C5L H41 H 8.815 0.02 1 82 23 11 C5L H42 H 6.266 0.02 1 83 23 11 C5L H6 H 7.553 0.02 1 84 23 11 C5L H7* H 1.317 0.02 1 85 23 11 C5L HCD* H 3.503 0.02 1 86 24 12 DG H1' H 6.079 0.02 1 stop_ save_