data_5776 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; sPrODN1:RNA [5'-R(AAAGGAGGA)-3'/5'-D(CXXXXXX)-3'] ; _BMRB_accession_number 5776 _BMRB_flat_file_name bmr5776.str _Entry_type original _Submission_date 2003-03-16 _Accession_date 2003-03-16 _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 Znosko B. M. . 2 Barnes T. W. III 3 Krugh T. R. . 4 Turner D. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 152 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-06-09 original author 'original release' 2010-07-16 update BMRB 'update DNA residue label to two-letter code' stop_ loop_ _Related_BMRB_accession_number _Relationship 5775 'unmodified DNA:RNA duplex' 5777 'modified PODN:RNA duplex' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR Studies of DNA Single Strands and DNA:RNA Hybrids With and Without 1-Propynylation at C5 of Oligopyrimidines ; _Citation_status published _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 Znosko B. M. . 2 Barnes T. W. III 3 Krugh T. R. . 4 Turner D. H. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_volume 125 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6090 _Page_last 6097 _Year 2003 _Details . loop_ _Keyword DNA hybrid propynyl RNA stop_ save_ ################################## # Molecular system description # ################################## save_system_Hybrid _Saveframe_category molecular_system _Mol_system_name sPrODN1:RNA _Abbreviation_common 'sPrODN1:RNA hybrid' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'RNA chain' $RNA 'sPrODN1 chain' $DNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state duplex _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 'sPrODN1 chain' _Abbreviation_common 'sPrODN1 chain' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence UAAAGGAGGAG loop_ _Residue_seq_code _Residue_label 1 U 2 A 3 A 4 A 5 G 6 G 7 A 8 G 9 G 10 A 11 G stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA chain' _Abbreviation_common 'DNA chain' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 7 _Mol_residue_sequence CXXXXXX loop_ _Residue_seq_code _Residue_label 1 DC 2 5PC 3 PDU 4 5PC 5 5PC 6 PDU 7 PDU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_PDU _Saveframe_category polymer_residue _Mol_type 'DNA linking' _Name_common 5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE _BMRB_code . _PDB_code PDU _Standard_residue_derivative . _Molecular_mass 350.262 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 16 11:37:45 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? 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 . ? 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 . ? C5A C5A C . 0 . ? C5B C5B C . 0 . ? C5M C5M C . 0 . ? C6 C6 C . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2'' H2'' H . 0 . ? H2' H2' H . 0 . ? H1' H1' H . 0 . ? H3 H3 H . 0 . ? H5A1 H5A1 H . 0 . ? H5A2 H5A2 H . 0 . ? H5B1 H5B1 H . 0 . ? H5B2 H5B2 H . 0 . ? H71 H71 H . 0 . ? H72 H72 H . 0 . ? H73 H73 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 OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? 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 C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2'' ? ? SING C2' H2' ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? SING N3 C4 ? ? SING N3 H3 ? ? DOUB C4 O4 ? ? SING C4 C5 ? ? SING C5 C5A ? ? DOUB C5 C6 ? ? SING C5A C5B ? ? SING C5A H5A1 ? ? SING C5A H5A2 ? ? SING C5B C5M ? ? SING C5B H5B1 ? ? SING C5B H5B2 ? ? SING C5M H71 ? ? SING C5M H72 ? ? SING C5M H73 ? ? SING C6 H6 ? ? stop_ save_ save_chem_comp_5PC _Saveframe_category polymer_residue _Mol_type 'DNA linking' _Name_common 5(1-PROPYNYL)-2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE _BMRB_code . _PDB_code 5PC _Standard_residue_derivative . _Molecular_mass 345.245 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Thu Jun 16 11:39:13 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons OP3 OP3 O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 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 . ? N4 N4 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? HOP3 HOP3 H . 0 . ? HOP2 HOP2 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H1' H1' H . 0 . ? H41 H41 H . 0 . ? H42 H42 H . 0 . ? H6 H6 H . 0 . ? H91 H91 H . 0 . ? H92 H92 H . 0 . ? H93 H93 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 OP3 P ? ? SING OP3 HOP3 ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P O5' ? ? SING OP2 HOP2 ? ? SING C5' O5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? 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' ? ? SING C2' H2'' ? ? SING C1' N1 ? ? SING C1' H1' ? ? SING N1 C2 ? ? SING N1 C6 ? ? DOUB C2 O2 ? ? SING C2 N3 ? ? DOUB N3 C4 ? ? SING C4 N4 ? ? SING C4 C5 ? ? SING N4 H41 ? ? SING N4 H42 ? ? DOUB C5 C6 ? ? SING C5 C7 ? ? SING C6 H6 ? ? TRIP C7 C8 ? ? SING C8 C9 ? ? SING C9 H91 ? ? SING C9 H92 ? ? SING C9 H93 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $RNA . . . . . . 'not applicable' $DNA . . . . . . 'not applicable' 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 $RNA 'chemical synthesis' . . . . . $DNA '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 $RNA 1 mM . $DNA 1 mM . NaCl 80 mM . 'phosphate buffer' 10 mM . EDTA 0.5 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 5.2 loop_ _Task collection stop_ _Details Varian save_ save_FELIX _Saveframe_category software _Name FELIX _Version 2000 loop_ _Task 'data analysis' stop_ _Details MSI save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 95.0 loop_ _Task refinement 'structure solution' stop_ _Details MSI save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _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 'ionic strength' 80 . mM pH 7.0 . n/a pressure 1 . atm temperature 273 . K stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 80 . mM pH 7.0 . n/a pressure 1 . atm temperature 303 . 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0 $entry_citation $entry_citation 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 'sPrODN1 chain' _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 H6 H 8.05 . 1 2 . 1 DC H5 H 6.08 . 1 3 . 1 DC H1' H 5.91 . 1 4 . 1 DC H2' H 2.76 . 1 5 . 1 DC H3' H 4.76 . 1 6 . 1 DC H4' H 4.27 . 1 7 . 1 DC H5' H 4.09 . 1 8 . 1 DC H2'' H 2.75 . 1 9 . 2 5PC H6 H 7.90 . 1 10 . 2 5PC H1' H 6.02 . 1 11 . 2 5PC H2' H 2.51 . 1 12 . 2 5PC H3' H 4.85 . 1 13 . 2 5PC H4' H 4.39 . 1 14 . 2 5PC H5' H 4.29 . 1 15 . 2 5PC H5'' H 4.19 . 1 16 . 2 5PC H2'' H 2.75 . 1 17 . 2 5PC H91 H 2.00 . 1 18 . 2 5PC H92 H 2.00 . 1 19 . 2 5PC H93 H 2.00 . 1 20 . 3 PDU H6 H 7.90 . 1 21 . 3 PDU H1' H 6.15 . 1 22 . 3 PDU H2' H 2.46 . 1 23 . 3 PDU H3' H 4.92 . 1 24 . 3 PDU H4' H 4.38 . 1 25 . 3 PDU H5' H 4.25 . 1 26 . 3 PDU H5'' H 4.19 . 1 27 . 3 PDU H2'' H 2.81 . 1 28 . 3 PDU H71 H 2.06 . 1 29 . 3 PDU H72 H 2.06 . 1 30 . 3 PDU H73 H 2.06 . 1 31 . 4 5PC H6 H 7.78 . 1 32 . 4 5PC H1' H 6.08 . 1 33 . 4 5PC H2' H 2.44 . 1 34 . 4 5PC H3' H 4.82 . 1 35 . 4 5PC H4' H 4.38 . 1 36 . 4 5PC H5' H 4.32 . 1 37 . 4 5PC H5'' H 4.20 . 1 38 . 4 5PC H2'' H 2.76 . 1 39 . 4 5PC H91 H 2.11 . 1 40 . 4 5PC H92 H 2.11 . 1 41 . 4 5PC H93 H 2.11 . 1 42 . 5 5PC H6 H 7.66 . 1 43 . 5 5PC H1' H 5.99 . 1 44 . 5 5PC H2' H 2.41 . 1 45 . 5 5PC H3' H 4.84 . 1 46 . 5 5PC H4' H 4.32 . 1 47 . 5 5PC H5' H 4.27 . 1 48 . 5 5PC H5'' H 4.19 . 1 49 . 5 5PC H2'' H 2.73 . 1 50 . 5 5PC H91 H 2.07 . 1 51 . 5 5PC H92 H 2.07 . 1 52 . 5 5PC H93 H 2.07 . 1 53 . 6 PDU H6 H 7.79 . 1 54 . 6 PDU H1' H 6.12 . 1 55 . 6 PDU H2' H 2.36 . 1 56 . 6 PDU H3' H 4.94 . 1 57 . 6 PDU H4' H 4.32 . 1 58 . 6 PDU H5' H 4.27 . 1 59 . 6 PDU H5'' H 4.17 . 1 60 . 6 PDU H2'' H 2.73 . 1 61 . 6 PDU H71 H 2.04 . 1 62 . 6 PDU H72 H 2.04 . 1 63 . 6 PDU H73 H 2.04 . 1 64 . 7 PDU H6 H 7.98 . 1 65 . 7 PDU H1' H 6.38 . 1 66 . 7 PDU H2' H 2.39 . 1 67 . 7 PDU H3' H 4.64 . 1 68 . 7 PDU H4' H 4.17 . 1 69 . 7 PDU H2'' H 2.38 . 1 70 . 7 PDU H71 H 2.07 . 1 71 . 7 PDU H72 H 2.07 . 1 72 . 7 PDU H73 H 2.07 . 1 stop_ save_ save_chemical_shift_set_2 _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 'RNA chain' _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 U H6 H 7.76 . 1 2 . 1 U H1' H 5.95 . 1 3 . 1 U H2' H 5.20 . 1 4 . 1 U H3' H 4.99 . 1 5 . 1 U H4' H 4.34 . 1 6 . 2 A H8 H 8.18 . 1 7 . 2 A H2 H 7.80 . 1 8 . 2 A H1' H 5.80 . 1 9 . 2 A H2' H 4.77 . 1 10 . 2 A H3' H 4.63 . 1 11 . 2 A H4' H 4.40 . 1 12 . 2 A H5' H 3.96 . 1 13 . 2 A H5'' H 3.90 . 1 14 . 3 A H8 H 8.12 . 1 15 . 3 A H2 H 7.58 . 1 16 . 3 A H1' H 5.70 . 1 17 . 3 A H2' H 4.77 . 1 18 . 3 A H3' H 4.75 . 1 19 . 3 A H4' H 4.55 . 1 20 . 3 A H5' H 4.24 . 1 21 . 3 A H5'' H 4.22 . 1 22 . 4 A H8 H 7.80 . 1 23 . 4 A H2 H 7.67 . 1 24 . 4 A H1' H 5.84 . 1 25 . 4 A H2' H 4.70 . 1 26 . 4 A H3' H 4.56 . 1 27 . 4 A H4' H 4.52 . 1 28 . 4 A H5' H 4.27 . 1 29 . 4 A H5'' H 4.25 . 1 30 . 5 G H8 H 7.15 . 1 31 . 5 G H1' H 5.63 . 1 32 . 5 G H2' H 4.62 . 1 33 . 5 G H3' H 4.41 . 1 34 . 5 G H4' H 4.48 . 1 35 . 5 G H5' H 4.11 . 1 36 . 5 G H5'' H 4.09 . 1 37 . 6 G H8 H 7.13 . 1 38 . 6 G H1' H 5.75 . 1 39 . 6 G H2' H 4.65 . 1 40 . 6 G H3' H 4.45 . 1 41 . 6 G H4' H 4.50 . 1 42 . 6 G H5' H 4.08 . 1 43 . 6 G H5'' H 4.06 . 1 44 . 7 A H8 H 7.66 . 1 45 . 7 A H2 H 7.53 . 1 46 . 7 A H1' H 6.04 . 1 47 . 7 A H2' H 4.74 . 1 48 . 7 A H3' H 4.60 . 1 49 . 7 A H4' H 4.53 . 1 50 . 7 A H5' H 4.13 . 1 51 . 7 A H5'' H 4.11 . 1 52 . 8 G H8 H 7.11 . 1 53 . 8 G H1' H 5.67 . 1 54 . 8 G H2' H 4.65 . 1 55 . 8 G H3' H 4.39 . 1 56 . 8 G H4' H 4.50 . 1 57 . 8 G H5' H 4.07 . 1 58 . 8 G H5'' H 4.06 . 1 59 . 9 G H8 H 7.10 . 1 60 . 9 G H1' H 5.77 . 1 61 . 9 G H2' H 4.63 . 1 62 . 9 G H3' H 4.45 . 1 63 . 9 G H4' H 4.50 . 1 64 . 9 G H5' H 4.08 . 1 65 . 9 G H5'' H 4.06 . 1 66 . 10 A H8 H 7.64 . 1 67 . 10 A H2 H 7.73 . 1 68 . 10 A H1' H 5.95 . 1 69 . 10 A H2' H 4.45 . 1 70 . 10 A H3' H 4.56 . 1 71 . 10 A H4' H 4.44 . 1 72 . 10 A H5' H 4.13 . 1 73 . 10 A H5'' H 4.11 . 1 74 . 11 G H8 H 7.58 . 1 75 . 11 G H1' H 5.64 . 1 76 . 11 G H2' H 4.33 . 1 77 . 11 G H3' H 4.45 . 1 78 . 11 G H4' H 4.25 . 1 79 . 11 G H5' H 4.08 . 1 80 . 11 G H5'' H 4.06 . 1 stop_ save_