data_18079 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; UNAC Tetraloops: To What Extent Can They Mimic GNRA Tetraloops ; _BMRB_accession_number 18079 _BMRB_flat_file_name bmr18079.str _Entry_type original _Submission_date 2011-11-14 _Accession_date 2011-11-14 _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 Zhao Q. . . 2 Huang H. . . 3 Nagaswamy U. . . 4 Xia Y. . . 5 Gao X. . . 6 Fox George E. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 90 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-05-22 original author . stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'UNAC tetraloops: to what extent do they mimic GNRA tetraloops?' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22605553 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhao Qin . . 2 Huang Hung-Chung . . 3 Nagaswamy Uma . . 4 Xia Youlin . . 5 Gao Xiaolian . . 6 Fox George E. . stop_ _Journal_abbreviation Biopolymers _Journal_name_full Biopolymers _Journal_volume 97 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 617 _Page_last 628 _Year 2012 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'UNAC Tetraloops' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label UNAC $UNAC stop_ _System_molecular_weight 7048.30396 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_UNAC _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 5'-R(*GP*GP*AP*CP*CP*CP*GP*GP*CP*UP*AP*AP*CP*GP_*CP*UP*GP*GP*GP*UP*CP*C)-3'_ _Molecular_mass 7048.30396 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; XGACCCGGCUAACGCUGGGU CC ; loop_ _Residue_seq_code _Residue_label 1 GMP 2 G 3 A 4 C 5 C 6 C 7 G 8 G 9 C 10 U 11 A 12 A 13 C 14 G 15 C 16 U 17 G 18 G 19 G 20 U 21 C 22 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 4A4R 4A4R . . . . . stop_ save_ ###################### # Polymer residues # ###################### save_chem_comp_GMP _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common GUANOSINE _BMRB_code . _PDB_code GMP _Standard_residue_derivative . _Molecular_mass 283.241 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Wed Nov 16 08:53:55 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons 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 . ? O2' O2' O . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? HO5' HO5' H . 0 . ? H5'1 H5'1 H . 0 . ? H5'2 H5'2 H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? HO2' HO2' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? HN1 HN1 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 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 O5' C5' ? ? SING O5' HO5' ? ? SING C5' C4' ? ? SING C5' H5'1 ? ? SING C5' H5'2 ? ? 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' O2' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING O2' HO2' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 HN1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N2 HN21 ? ? SING N2 HN22 ? ? SING N3 C4 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $UNAC 'Haloarcula marismortui' 2238 Bacteria . Haloarcula marismortui stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $UNAC 'chemical synthesis' . . . . n/a . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.3 mM' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $UNAC 0.3 mM '[U-13C; U-15N]' D2O 99.96 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AutoDep _Saveframe_category software _Name AutoDep _Version 4.3 loop_ _Vendor _Address _Electronic_address AutoDep . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version any loop_ _Vendor _Address _Electronic_address BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 0 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details 'pH [7.0], temp [298], pressure [0.0], ionStrength [0.0]' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.000 . pH pressure 1 . atm temperature 298.000 . K 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 HDO H 1 protons ppm 4.7 internal 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 _Saveframe_category assigned_chemical_shifts _Details 'Origin nmrStar file /ebi/msd/pdb_root/Processing/prepare/4a4r/ebi/UAAC.ppm.csh' loop_ _Experiment_label '2D NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name UNAC _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 GMP H1' H 5.511 . 1 2 1 1 GMP H8 H 8.141 . 1 3 2 2 G H1' H 5.191 . 1 4 2 2 G H8 H 7.451 . 1 5 3 3 A H1' H 5.957 0.001 1 6 3 3 A H2' H 4.511 . 1 7 3 3 A H3' H 4.101 . 1 8 3 3 A H8 H 7.877 0.003 1 9 4 4 C H1' H 5.325 0.005 1 10 4 4 C H2' H 4.264 0.003 1 11 4 4 C H3' H 3.987 0.005 1 12 4 4 C H5 H 5.175 0.006 1 13 4 4 C H6 H 7.361 0.005 1 14 5 5 C H2' H 3.888 . 1 15 5 5 C H5 H 5.390 0.01 1 16 5 5 C H6 H 7.756 0.023 1 17 6 6 C H1' H 5.440 . 1 18 6 6 C H2' H 4.025 0.001 1 19 6 6 C H5 H 5.455 0.002 1 20 6 6 C H6 H 7.720 0.016 1 21 7 7 G H1' H 5.664 0.003 1 22 7 7 G H2' H 4.012 0.006 1 23 7 7 G H3' H 4.216 0.016 1 24 7 7 G H8 H 7.428 0.004 1 25 8 8 G H1' H 5.683 0.003 1 26 8 8 G H2' H 4.360 . 1 27 8 8 G H3' H 4.269 . 1 28 8 8 G H4' H 4.001 . 1 29 8 8 G H8 H 7.185 0.015 1 30 9 9 C H1' H 5.564 0.829 1 31 9 9 C H2' H 4.330 . 1 32 9 9 C H3' H 4.452 . 1 33 9 9 C H5 H 5.040 0.008 1 34 9 9 C H6 H 7.354 0.032 1 35 10 10 U H1' H 5.467 0.001 1 36 10 10 U H2' H 4.332 0.011 1 37 10 10 U H3' H 4.416 . 1 38 10 10 U H5 H 5.583 0.032 1 39 10 10 U H6 H 7.491 0.005 1 40 11 11 A H1' H 5.649 0.009 1 41 11 11 A H2' H 4.191 0.006 1 42 11 11 A H3' H 4.966 0.01 1 43 11 11 A H4' H 4.214 . 1 44 11 11 A H8 H 8.299 0.004 1 45 12 12 A H1' H 5.747 0.001 1 46 12 12 A H2' H 4.230 . 1 47 12 12 A H3' H 3.911 . 1 48 12 12 A H4' H 4.305 . 1 49 12 12 A H8 H 7.945 0.008 1 50 13 13 C H1' H 5.204 . 1 51 13 13 C H2' H 4.406 . 1 52 13 13 C H3' H 4.071 . 1 53 13 13 C H5 H 5.253 0.008 1 54 13 13 C H6 H 7.664 0.003 1 55 14 14 G H1' H 4.861 0.004 1 56 14 14 G H2' H 4.203 0.009 1 57 14 14 G H3' H 4.395 0.004 1 58 14 14 G H4' H 4.265 . 1 59 14 14 G H5' H 4.248 . 1 60 14 14 G H8 H 7.801 0.007 1 61 15 15 C H1' H 5.646 . 1 62 15 15 C H2' H 4.262 0.004 1 63 15 15 C H5 H 5.194 0.007 1 64 15 15 C H6 H 7.531 0.024 1 65 16 16 U H1' H 5.661 . 1 66 16 16 U H2' H 4.408 0.008 1 67 16 16 U H5 H 5.640 0.003 1 68 16 16 U H6 H 7.705 0.013 1 69 17 17 G H1' H 5.697 0.006 1 70 17 17 G H2' H 4.421 . 1 71 17 17 G H3' H 3.987 . 1 72 17 17 G H8 H 7.148 0.009 1 73 18 18 G H1' H 5.676 . 1 74 18 18 G H8 H 7.826 0.008 1 75 19 19 G H1' H 5.716 0.002 1 76 19 19 G H2' H 4.392 . 1 77 19 19 G H8 H 7.573 . 1 78 20 20 U H1' H 5.563 . 1 79 20 20 U H2' H 4.321 . 1 80 20 20 U H5 H 5.026 0.006 1 81 20 20 U H6 H 7.722 0.002 1 82 21 21 C H1' H 5.462 0.012 1 83 21 21 C H2' H 4.363 . 1 84 21 21 C H5 H 5.624 0.001 1 85 21 21 C H6 H 7.836 . 1 86 22 22 C H1' H 5.668 0.011 1 87 22 22 C H2' H 3.913 . 1 88 22 22 C H3' H 4.136 . 1 89 22 22 C H5 H 5.535 . 1 90 22 22 C H6 H 7.614 0.01 1 stop_ save_