data_6979 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs ; _BMRB_accession_number 6979 _BMRB_flat_file_name bmr6979.str _Entry_type original _Submission_date 2006-02-09 _Accession_date 2006-02-09 _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 Chen G. . . 2 Kennedy S. D. . 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" 168 "31P chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2006-06-26 original author . stop_ _Original_release_date 2006-06-26 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; An Alternating Sheared AA Pair and Elements of Stability for a Single Sheared Purine-Purine Pair Flanked by Sheared GA Pairs in RNA ; _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 Chen Gang . . 2 Kennedy Scott D. . 3 Qiao Jing . . 4 Krugh Thomas R. . 5 Turner Douglas H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 45 _Journal_issue 22 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6889 _Page_last 6903 _Year 2006 _Details . loop_ _Keyword 'alternating sheared AA pair' 'Kink-turn motif' 'rapid conformation exchange' 'RNA secondary structure prediction' 'sequence specific A-minor motif' thermodynamics stop_ save_ ################################## # Molecular system description # ################################## save_system_RNA _Saveframe_category molecular_system _Mol_system_name 5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3'/5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(PR5))-3' _Abbreviation_common 5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3'/5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(PR5))-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3' $GGUGAAGGCU 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(PR5))-3' $GCCGAAGCCP stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_GGUGAAGGCU _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common GGUGAAGGCU _Abbreviation_common GGUGAAGGCU _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence GGUGAAGGCU loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 U 4 G 5 A 6 A 7 G 8 G 9 C 10 U stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_GCCGAAGCCP _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common GCCGAAGCCP _Abbreviation_common GCCGAAGCCP _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence GCCGAAGCCX loop_ _Residue_seq_code _Residue_label 1 G 2 C 3 C 4 G 5 A 6 A 7 G 8 C 9 C 10 P5P stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_P5P _Saveframe_category polymer_residue _Mol_type 'RNA LINKING' _Name_common 'PURINE RIBOSIDE-5'-MONOPHOSPHATE' _BMRB_code . _PDB_code P5P _Standard_residue_derivative . _Molecular_mass 332.207 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Sep 19 14:27:51 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N1 N1 N . 0 . ? C2 C2 C . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? N7 N7 N . 0 . ? C8 C8 C . 0 . ? N9 N9 N . 0 . ? C1' C1' C . 0 . ? C2' C2' C . 0 . ? O2' O2' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C5' C5' C . 0 . ? O5' O5' O . 0 . ? P P P . 0 . ? OP1 OP1 O . 0 . ? OP2 OP2 O . 0 . ? OP3 OP3 O . 0 . ? H2 H2 H . 0 . ? H6 H6 H . 0 . ? H8 H8 H . 0 . ? H1' H1' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H4' H4' H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? HOP2 HOP2 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 SING N1 C2 ? ? DOUB N1 C6 ? ? DOUB C2 N3 ? ? SING C2 H2 ? ? SING N3 C4 ? ? DOUB C4 C5 ? ? SING C4 N9 ? ? SING C5 C6 ? ? SING C5 N7 ? ? SING C6 H6 ? ? DOUB N7 C8 ? ? SING C8 N9 ? ? SING C8 H8 ? ? SING N9 C1' ? ? SING C1' C2' ? ? SING C1' O4' ? ? SING C1' H1' ? ? SING C2' O2' ? ? SING C2' C3' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING C3' O3' ? ? SING C3' C4' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C4' O4' ? ? SING C4' C5' ? ? SING C4' H4' ? ? SING C5' O5' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? SING O5' P ? ? DOUB P OP1 ? ? SING P OP2 ? ? SING P OP3 ? ? SING OP2 HOP2 ? ? 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 $GGUGAAGGCU . . . . . . $GCCGAAGCCP . . . . . . 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 $GGUGAAGGCU 'chemical synthesis' . . . . . ; The molecules are synthsized chemically (phosphoramidite method) and they occur naturally as part of larger functional RNAs. ; $GCCGAAGCCP 'chemical synthesis' . . . . . ; The molecules are synthsized chemically (phosphoramidite method) and they occur naturally as part of larger functional RNAs. ; 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 $GGUGAAGGCU 2 mM . $GCCGAAGCCP 2 mM . NaCl 80 mM . 'sodium phosphate' 10 mM . Na2EDTA 0.5 mM . stop_ save_ ############################ # Computer software used # ############################ save_FELIX _Saveframe_category software _Name FELIX _Version . _Details . save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version . _Details refinement save_ save_VNMR _Saveframe_category software _Name VNMR _Version . _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save__1 _Saveframe_category NMR_applied_experiment _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.1 . pH temperature 303 . K stop_ save_ save_sample_cond_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.1 . pH temperature 278 . 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 TSP H 1 'methyl protons' ppm 0.0 external . . . . 1.0 $entry_citation $entry_citation '85% H3PO4' P 31 phosphorus ppm 0.0 external . . . . 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 'Imino and amino proton were assigned at 5 degC.' loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 5'-R(*GP*GP*UP*GP*AP*AP*GP*GP*CP*U)-3' _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 G H8 H 8.14 0.01 1 2 . 1 G H1' H 5.94 0.01 1 3 . 1 G H2' H 4.87 0.01 1 4 . 1 G H3' H 4.55 0.01 1 5 . 1 G H4' H 4.47 0.01 1 6 . 1 G H5' H 4.13 0.01 2 7 . 1 G H5'' H 4.00 0.01 2 8 . 1 G H1 H 11.93 0.01 1 9 . 2 G H8 H 7.32 0.01 1 10 . 2 G H1' H 5.77 0.01 1 11 . 2 G H2' H 4.65 0.01 1 12 . 2 G H3' H 4.42 0.01 1 13 . 2 G H4' H 4.47 0.01 1 14 . 2 G H5' H 4.55 0.01 2 15 . 2 G H5'' H 4.14 0.01 2 16 . 2 G H1 H 13.34 0.01 1 17 . 2 G P P 0.44 0.01 1 18 . 3 U H6 H 7.23 0.01 1 19 . 3 U H5 H 5.26 0.01 1 20 . 3 U H1' H 5.20 0.01 1 21 . 3 U H2' H 4.44 0.01 1 22 . 3 U H3' H 4.21 0.01 1 23 . 3 U H4' H 4.38 0.01 1 24 . 3 U H5' H 4.06 0.01 1 25 . 3 U H3 H 11.49 0.01 1 26 . 3 U P P 0.09 0.01 1 27 . 4 G H8 H 7.90 0.01 1 28 . 4 G H1' H 5.35 0.01 1 29 . 4 G H2' H 3.67 0.01 1 30 . 4 G H3' H 4.82 0.01 1 31 . 4 G H4' H 4.40 0.01 1 32 . 4 G H5' H 4.48 0.01 2 33 . 4 G H5'' H 4.15 0.01 2 34 . 4 G P P 0.56 0.01 1 35 . 5 A H8 H 8.24 0.01 1 36 . 5 A H2 H 8.28 0.01 1 37 . 5 A H1' H 5.68 0.01 1 38 . 5 A H2' H 4.95 0.01 1 39 . 5 A H3' H 4.82 0.01 1 40 . 5 A H4' H 4.65 0.01 1 41 . 5 A H5' H 4.45 0.01 2 42 . 5 A H5'' H 4.16 0.01 2 43 . 5 A P P 0.05 0.01 1 44 . 6 A H8 H 7.62 0.01 1 45 . 6 A H2 H 7.94 0.01 1 46 . 6 A H1' H 5.44 0.01 1 47 . 6 A H2' H 4.74 0.01 1 48 . 6 A H3' H 4.40 0.01 1 49 . 6 A H5' H 4.47 0.01 2 50 . 6 A H5'' H 4.25 0.01 2 51 . 6 A P P 2.20 0.01 1 52 . 7 G H8 H 7.47 0.01 1 53 . 7 G H1' H 4.27 0.01 1 54 . 7 G H2' H 4.33 0.01 1 55 . 7 G H3' H 4.37 0.01 1 56 . 7 G H4' H 4.40 0.01 1 57 . 7 G H5' H 4.47 0.01 2 58 . 7 G H5'' H 4.10 0.01 2 59 . 7 G H1 H 12.61 0.01 1 60 . 7 G P P 0.18 0.01 1 61 . 8 G H8 H 7.13 0.01 1 62 . 8 G H1' H 5.71 0.01 1 63 . 8 G H2' H 4.49 0.01 1 64 . 8 G H3' H 4.39 0.01 1 65 . 8 G H4' H 4.43 0.01 1 66 . 8 G H5' H 4.27 0.01 2 67 . 8 G H5'' H 4.01 0.01 2 68 . 8 G H1 H 13.22 0.01 1 69 . 8 G P P 0.11 0.01 1 70 . 9 C H6 H 7.42 0.01 1 71 . 9 C H5 H 5.12 0.01 1 72 . 9 C H1' H 5.59 0.01 1 73 . 9 C H2' H 4.37 0.01 1 74 . 9 C H3' H 4.26 0.01 1 75 . 9 C H4' H 4.39 0.01 1 76 . 9 C H5' H 4.16 0.01 2 77 . 9 C H5'' H 4.03 0.01 2 78 . 9 C H41 H 8.47 0.01 1 79 . 9 C H42 H 7.08 0.01 1 80 . 9 C P P 0.39 0.01 1 81 . 10 U H6 H 7.74 0.01 1 82 . 10 U H5 H 5.55 0.01 1 83 . 10 U H1' H 5.73 0.01 1 84 . 10 U H2' H 3.96 0.01 1 85 . 10 U H3' H 4.16 0.01 1 86 . 10 U H4' H 4.14 0.01 1 87 . 10 U H5' H 4.31 0.01 2 88 . 10 U H5'' H 4.03 0.01 2 89 . 10 U H3 H 10.95 0.01 1 90 . 10 U P P 0.25 0.01 1 stop_ save_ save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details 'Imino and amino proton were assigned at 5 degC.' loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 5'-R(*GP*CP*CP*GP*AP*AP*GP*CP*CP*(PR5))-3' _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 G H8 H 8.11 0.01 1 2 . 1 G H1' H 5.86 0.01 1 3 . 1 G H2' H 4.83 0.01 1 4 . 1 G H3' H 4.54 0.01 1 5 . 1 G H4' H 4.44 0.01 1 6 . 1 G H5' H 4.13 0.01 2 7 . 1 G H5'' H 3.96 0.01 2 8 . 1 G H1 H 13.35 0.01 1 9 . 2 C H6 H 7.83 0.01 1 10 . 2 C H5 H 5.25 0.01 1 11 . 2 C H1' H 5.65 0.01 1 12 . 2 C H2' H 4.57 0.01 1 13 . 2 C H3' H 4.49 0.01 1 14 . 2 C H4' H 4.50 0.01 1 15 . 2 C H5' H 4.43 0.01 2 16 . 2 C H5'' H 4.16 0.01 2 17 . 2 C H41 H 8.72 0.01 1 18 . 2 C H42 H 6.89 0.01 1 19 . 2 C P P 0.09 0.01 1 20 . 3 C H6 H 7.41 0.01 1 21 . 3 C H5 H 5.32 0.01 1 22 . 3 C H1' H 5.45 0.01 1 23 . 3 C H2' H 4.48 0.01 1 24 . 3 C H3' H 4.24 0.01 1 25 . 3 C H4' H 4.43 0.01 1 26 . 3 C H5' H 4.45 0.01 2 27 . 3 C H5'' H 4.13 0.01 2 28 . 3 C H41 H 8.10 0.01 1 29 . 3 C H42 H 6.59 0.01 1 30 . 3 C P P 0.62 0.01 1 31 . 4 G H8 H 7.92 0.01 1 32 . 4 G H1' H 5.55 0.01 1 33 . 4 G H2' H 4.24 0.01 1 34 . 4 G H3' H 4.92 0.01 1 35 . 4 G H4' H 4.50 0.01 1 36 . 4 G H5' H 4.41 0.01 2 37 . 4 G H5'' H 4.13 0.01 2 38 . 4 G P P 0.21 0.01 1 39 . 5 A H8 H 8.16 0.01 1 40 . 5 A H2 H 7.83 0.01 1 41 . 5 A H1' H 5.72 0.01 1 42 . 5 A H2' H 4.92 0.01 1 43 . 5 A H3' H 4.80 0.01 1 44 . 5 A H4' H 4.59 0.01 1 45 . 5 A H5' H 4.52 0.01 2 46 . 5 A H5'' H 4.22 0.01 2 47 . 5 A P P 0.28 0.01 1 48 . 6 A H8 H 7.52 0.01 1 49 . 6 A H2 H 8.06 0.01 1 50 . 6 A H1' H 5.42 0.01 1 51 . 6 A H2' H 4.80 0.01 1 52 . 6 A H3' H 4.36 0.01 1 53 . 6 A H4' H 4.52 0.01 1 54 . 6 A H5' H 4.47 0.01 2 55 . 6 A H5'' H 4.21 0.01 2 56 . 6 A P P 1.41 0.01 1 57 . 7 G H8 H 7.32 0.01 1 58 . 7 G H1' H 4.70 0.01 1 59 . 7 G H2' H 4.33 0.01 1 60 . 7 G H3' H 4.37 0.01 1 61 . 7 G H1 H 11.46 0.01 1 62 . 7 G H21 H 6.36 0.01 1 63 . 7 G H22 H 5.40 0.01 1 64 . 7 G P P 0.17 0.01 1 65 . 8 C H6 H 7.59 0.01 1 66 . 8 C H5 H 5.37 0.01 1 67 . 8 C H1' H 5.41 0.01 1 68 . 8 C H2' H 4.19 0.01 1 69 . 8 C H3' H 4.43 0.01 1 70 . 8 C H4' H 4.36 0.01 1 71 . 8 C H5' H 4.09 0.01 2 72 . 8 C H5'' H 4.04 0.01 2 73 . 8 C H41 H 8.29 0.01 1 74 . 8 C H42 H 7.06 0.01 1 75 . 8 C P P 0.23 0.01 1 76 . 9 C H6 H 7.65 0.01 1 77 . 9 C H5 H 5.44 0.01 1 78 . 9 C H1' H 5.48 0.01 1 79 . 9 C H2' H 4.36 0.01 1 80 . 9 C H3' H 4.48 0.01 1 81 . 9 C H4' H 4.37 0.01 1 82 . 9 C H5' H 4.29 0.01 2 83 . 9 C H5'' H 4.08 0.01 2 84 . 9 C H41 H 8.06 0.01 1 85 . 9 C H42 H 7.07 0.01 1 86 . 9 C P P 0.34 0.01 1 87 . 10 P5P H2 H 8.13 0.01 1 88 . 10 P5P H6 H 8.84 0.01 1 89 . 10 P5P H8 H 8.44 0.01 1 90 . 10 P5P H1' H 6.15 0.01 1 91 . 10 P5P H2' H 4.17 0.01 1 92 . 10 P5P H3' H 4.33 0.01 1 93 . 10 P5P H4' H 4.31 0.01 1 94 . 10 P5P H5'1 H 4.44 0.01 2 95 . 10 P5P H5'2 H 4.10 0.01 2 96 . 10 P5P P P 0.38 0.01 1 stop_ save_