data_5587 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Molecular Recognition in Purine-Rich Internal Loops: Thermodynamic, Structural, and Dynamic Consequences of Purine for Adenine Substitutions in 5'(rGGCAAGCCU)2 ; _BMRB_accession_number 5587 _BMRB_flat_file_name bmr5587.str _Entry_type original _Submission_date 2002-11-13 _Accession_date 2002-11-14 _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 Burkard M. E. . 3 Krugh T. R. . 4 Turner D. H. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 77 "31P chemical shifts" 8 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2002-12-27 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 5586 'related molecule 5'-R(*GP*GP*CP*(P5P)P*AP*GP*CP*CP*U)-3'' 5588 'related molecule 5'-R(*GP*GP*CP*(P5P)P*(P5P)P*GP*CP*CP*U)-3'' 5614 'related molecule 5'-R(*GP*GP*CP*AP*AP*GP*CP*CP*U)-3'' stop_ _Original_release_date 2002-12-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Molecular Recognition in Purine-Rich Internal Loops: Thermodynamic, Structural, and Dynamic Consequences of Purine for Adenine Substitutions in 5'(rGGCAAGCCU)2 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22363258 _PubMed_ID 1245247 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Znosko B. M. . 2 Burkard M. E. . 3 Krugh T. R. . 4 Turner D. H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 41 _Journal_issue 50 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14978 _Page_last 14987 _Year 2002 _Details . loop_ _Keyword duplex purine 'ribonucleic acid' 'tandem mismatch' stop_ save_ ################################## # Molecular system description # ################################## save_system_Purine_Rich_Internal_Loop_RNA _Saveframe_category molecular_system _Mol_system_name 5'-R(*GP*GP*CP*AP*(P5P)P*GP*CP*CP*U)-3' _Abbreviation_common na _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-R(*GP*GP*CP*AP*(P5P)P*GP*CP*CP*U)-3' $PRIL_RNA 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_PRIL_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common na _Abbreviation_common na _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence GGCAXGCCU loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 A 5 P5P 6 G 7 C 8 C 9 U 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 Jul 25 13:33:28 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 $PRIL_RNA . . . . . . 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 $PRIL_RNA '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 $PRIL_RNA 1 mM . NaCl 80 mM . 'phosphate buffer' 10 mM . EDTA 0.5 mM . H2O 90 % . D2O 10 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $PRIL_RNA 2 mM . NaCl 80 mM . 'phosphate buffer' 10 mM . EDTA 0.5 mM . D2O 99.996 % . 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 '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 . 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 pH 6.5 . 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 pH 7.7 . 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 5'-R(*GP*GP*CP*AP*(P5P)P*GP*CP*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 H1 H 12.9 . 1 2 . 1 G H5'' H 3.99 . 2 3 . 1 G H5' H 4.12 . 2 4 . 1 G H4' H 4.47 . 1 5 . 1 G H3' H 4.62 . 1 6 . 1 G H2' H 4.95 . 1 7 . 1 G H1' H 5.88 . 1 8 . 1 G H8 H 8.1 . 1 9 . 2 G H1 H 13.3 . 1 10 . 2 G P P -1.8 . 1 11 . 2 G H5'' H 4.2 . 2 12 . 2 G H5' H 4.61 . 2 13 . 2 G H4' H 4.55 . 1 14 . 2 G H3' H 4.64 . 1 15 . 2 G H2' H 4.61 . 1 16 . 2 G H1' H 5.9 . 1 17 . 2 G H8 H 7.55 . 1 18 . 3 C H42 H 7.0 . 1 19 . 3 C H41 H 8.2 . 1 20 . 3 C P P -1.82 . 1 21 . 3 C H5'' H 4.14 . 2 22 . 3 C H5' H 4.57 . 2 23 . 3 C H4' H 4.56 . 1 24 . 3 C H3' H 4.46 . 1 25 . 3 C H2' H 4.55 . 1 26 . 3 C H1' H 5.52 . 1 27 . 3 C H5 H 5.19 . 1 28 . 3 C H6 H 7.48 . 1 29 . 4 A P P -2.36 . 1 30 . 4 A H5'' H 4.23 . 2 31 . 4 A H5' H 4.5 . 2 32 . 4 A H4' H 4.54 . 1 33 . 4 A H3' H 4.79 . 1 34 . 4 A H2' H 4.63 . 1 35 . 4 A H1' H 5.97 . 1 36 . 4 A H2 H 7.49 . 1 37 . 4 A H8 H 8.17 . 1 38 . 5 P5P P P -2.08 . 1 39 . 5 P5P H5'' H 4.03 . 2 40 . 5 P5P H5' H 4.39 . 2 41 . 5 P5P H4' H 4.24 . 1 42 . 5 P5P H3' H 4.63 . 1 43 . 5 P5P H2' H 4.67 . 1 44 . 5 P5P H1' H 5.99 . 1 45 . 5 P5P H2 H 8.7 . 1 46 . 5 P5P H8 H 8.4 . 1 47 . 5 P5P H6 H 9.03 . 1 48 . 6 G H1 H 12.8 . 1 49 . 6 G P P -1.93 . 1 50 . 6 G H5' H 4.14 . 2 51 . 6 G H4' H 4.3 . 1 52 . 6 G H3' H 4.38 . 1 53 . 6 G H2' H 4.46 . 1 54 . 6 G H1' H 5.49 . 1 55 . 6 G H8 H 7.5 . 1 56 . 7 C H42 H 6.9 . 1 57 . 7 C H41 H 8.6 . 1 58 . 7 C P P -1.87 . 1 59 . 7 C H5'' H 4.08 . 2 60 . 7 C H5' H 4.46 . 2 61 . 7 C H4' H 4.14 . 1 62 . 7 C H3' H 4.42 . 1 63 . 7 C H2' H 4.37 . 1 64 . 7 C H1' H 5.5 . 1 65 . 7 C H5 H 5.15 . 1 66 . 7 C H6 H 7.64 . 1 67 . 8 C H42 H 7.0 . 1 68 . 8 C H41 H 8.5 . 1 69 . 8 C P P -2.09 . 1 70 . 8 C H5'' H 4.07 . 2 71 . 8 C H5' H 4.5 . 2 72 . 8 C H4' H 4.54 . 1 73 . 8 C H3' H 4.31 . 1 74 . 8 C H2' H 4.35 . 1 75 . 8 C H1' H 5.58 . 1 76 . 8 C H5 H 5.44 . 1 77 . 8 C H6 H 7.63 . 1 78 . 9 U P P -1.92 . 1 79 . 9 U H5'' H 4.03 . 2 80 . 9 U H5' H 4.34 . 2 81 . 9 U H3' H 4.16 . 1 82 . 9 U H2' H 3.96 . 1 83 . 9 U H1' H 5.69 . 1 84 . 9 U H5 H 5.56 . 1 85 . 9 U H6 H 7.74 . 1 stop_ save_