data_7230 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from its Structure in Crystals of the 50S Ribosomal Subunit ; _BMRB_accession_number 7230 _BMRB_flat_file_name bmr7230.str _Entry_type original _Submission_date 2006-07-14 _Accession_date 2006-07-26 _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 Shankar N. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 102 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2006-10-19 original author . stop_ _Original_release_date 2006-10-19 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The NMR Structure of an Internal Loop from 23S Ribosomal RNA Differs from Its Structure in Crystals of 50S Ribosomal Subunits ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17002278 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Shankar Neelaabh . . 2 Kennedy S. D. . 3 Chen G. . . 4 Krugh T. R. . 5 Turner D. H. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 45 _Journal_issue 39 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 11776 _Page_last 11789 _Year 2006 _Details . loop_ _Keyword 'COMPARISON BETWEEN CRYSTAL STRUCTURE AND NMR STRUCTURE' 'RNA INTERNAL LOOP 5'cUAAg3'/3'gAAGc5'' 'THERMODYNAMICS OF INTERNAL LOOP' stop_ save_ ################################## # Molecular system description # ################################## save_system_RNA _Saveframe_category molecular_system _Mol_system_name '5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3', 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3'' _Abbreviation_common "5' CUAAG 3' / 3' GAAGC 5'" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3' $GGCUAAGAC 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3' $GUCGAAGCC 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_GGCUAAGAC _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3' _Abbreviation_common 5'-R(*GP*GP*CP*UP*AP*AP*GP*AP*C)-3' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence GGCUAAGAC loop_ _Residue_seq_code _Residue_label 1 G 2 G 3 C 4 U 5 A 6 A 7 G 8 A 9 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_GUCGAAGCC _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3' _Abbreviation_common 5'-R(*GP*UP*CP*GP*AP*AP*GP*CP*C)-3' _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 9 _Mol_residue_sequence GUCGAAGCC loop_ _Residue_seq_code _Residue_label 1 G 2 U 3 C 4 G 5 A 6 A 7 G 8 C 9 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $GGCUAAGAC 'Deinococcus radiodurans' 1299 Eubacteria . Deinococcus radiodurans 'Also found in 23S ribosomal subunit of Escherichia coli.' $GUCGAAGCC 'Deinococcus radiodurans' 1299 Eubacteria . Deinococcus radiodurans 'Also found in 23S ribosomal subunit of Escherichia coli.' 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 $GGCUAAGAC 'chemical synthesis' . . . . . 'RNA chemical synthesis' $GUCGAAGCC 'chemical synthesis' . . . . . '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 $GGCUAAGAC 2 mM . $GUCGAAGCC 2 mM . NaCl 80 mM . 'SODIUM PHOSPHATE' 10 mM . Na2EDTA 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 $GGCUAAGAC 2 mM . $GUCGAAGCC 2 mM . NaCl 80 mM . 'SODIUM PHOSPHATE' 10 mM . Na2EDTA 0.5 mM . D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.110 loop_ _Task 'data analysis' stop_ _Details 'T. D. Goddard and D. G. Kneller' save_ save_NMRDraw _Saveframe_category software _Name NMRDraw _Version 2.3 loop_ _Task processing stop_ _Details 'F. Delaglio' save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 98 loop_ _Task refinement stop_ _Details 'Molecular Simulations Inc.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_unknown_1 _Saveframe_category NMR_applied_experiment _Experiment_name unknown _Sample_label . 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 . pH temperature 298 . 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 H2O H 1 protons ppm 4.788 internal direct cylindrical internal perpendicular 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 'Exchangeable protons were assigned at 10 C.' loop_ _Experiment_label unknown stop_ 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*UP*AP*AP*GP*AP*C)-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 7.912 . . 2 . 1 G H1' H 5.640 . . 3 . 1 G H2' H 4.808 . . 4 . 1 G H3' H 4.507 . . 5 . 1 G H4' H 3.938 . . 6 . 1 G H1 H 12.57 . . 7 . 2 G H8 H 7.477 . . 8 . 2 G H1' H 5.873 . . 9 . 2 G H2' H 4.579 . . 10 . 2 G H3' H 4.532 . . 11 . 2 G H1 H 13.37 . . 12 . 3 C H6 H 7.394 . . 13 . 3 C H5 H 5.109 . . 14 . 3 C H1' H 5.465 . . 15 . 3 C H2' H 4.623 . . 16 . 3 C H3' H 4.273 . . 17 . 3 C H41 H 8.247 . . 18 . 3 C H42 H 6.817 . . 19 . 4 U H6 H 7.841 . . 20 . 4 U H5 H 5.519 . . 21 . 4 U H1' H 5.489 . . 22 . 4 U H2' H 4.012 . . 23 . 4 U H3' H 4.518 . . 24 . 4 U H4' H 4.376 . . 25 . 4 U H3 H 11.60 . . 26 . 5 A H8 H 8.405 . . 27 . 5 A H2 H 8.671 . . 28 . 5 A H1' H 5.731 . . 29 . 5 A H2' H 4.629 . . 30 . 5 A H3' H 4.862 . . 31 . 5 A H4' H 4.676 . . 32 . 6 A H8 H 7.793 . . 33 . 6 A H2 H 7.692 . . 34 . 6 A H1' H 5.784 . . 35 . 6 A H2' H 4.587 . . 36 . 6 A H3' H 4.412 . . 37 . 6 A H4' H 4.285 . . 38 . 7 G H8 H 7.414 . . 39 . 7 G H1' H 3.822 . . 40 . 7 G H2' H 4.272 . . 41 . 7 G H4' H 4.293 . . 42 . 7 G H1 H 12.35 . . 43 . 8 A H8 H 7.668 . . 44 . 8 A H2 H 7.780 . . 45 . 8 A H1' H 5.918 . . 46 . 8 A H2' H 4.437 . . 47 . 8 A H3' H 4.568 . . 48 . 9 C H6 H 7.307 . . 49 . 9 C H5 H 5.152 . . 50 . 9 C H1' H 5.617 . . 51 . 9 C H2' H 3.933 . . 52 . 9 C H3' H 4.230 . . stop_ save_ save_chemical_shift_set_2 _Saveframe_category assigned_chemical_shifts _Details 'Exchangeable protons were assigned at 10 C.' 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*UP*CP*GP*AP*AP*GP*CP*C)-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 5.618 . . 2 . 1 G H2' H 4.672 . . 3 . 1 G H1 H 12.95 . . 4 . 2 U H6 H 7.926 . . 5 . 2 U H5 H 5.005 . . 6 . 2 U H1' H 5.639 . . 7 . 2 U H2' H 4.614 . . 8 . 2 U H3' H 4.472 . . 9 . 2 U H3 H 14.46 . . 10 . 3 C H6 H 7.577 . . 11 . 3 C H5 H 5.395 . . 12 . 3 C H1' H 5.474 . . 13 . 3 C H2' H 4.621 . . 14 . 3 C H3' H 4.321 . . 15 . 3 C H41 H 8.012 . . 16 . 3 C H42 H 6.449 . . 17 . 4 G H8 H 8.067 . . 18 . 4 G H1' H 5.557 . . 19 . 4 G H2' H 4.423 . . 20 . 4 G H3' H 5.010 . . 21 . 4 G H4' H 4.536 . . 22 . 4 G H1 H 10.20 . . 23 . 5 A H8 H 8.128 . . 24 . 5 A H2 H 7.844 . . 25 . 5 A H1' H 5.849 . . 26 . 5 A H2' H 4.949 . . 27 . 5 A H3' H 4.681 . . 28 . 5 A H4' H 4.601 . . 29 . 6 A H8 H 7.690 . . 30 . 6 A H2 H 7.678 . . 31 . 6 A H1' H 5.038 . . 32 . 6 A H2' H 4.473 . . 33 . 6 A H3' H 4.443 . . 34 . 7 G H8 H 6.842 . . 35 . 7 G H1' H 5.254 . . 36 . 7 G H2' H 4.373 . . 37 . 7 G H3' H 4.328 . . 38 . 7 G H1 H 13.04 . . 39 . 8 C H6 H 7.645 . . 40 . 8 C H5 H 5.099 . . 41 . 8 C H1' H 5.510 . . 42 . 8 C H2' H 4.292 . . 43 . 8 C H3' H 4.444 . . 44 . 8 C H41 H 8.513 . . 45 . 8 C H42 H 6.855 . . 46 . 9 C H6 H 7.662 . . 47 . 9 C H5 H 5.512 . . 48 . 9 C H1' H 5.720 . . 49 . 9 C H2' H 4.056 . . 50 . 9 C H4' H 4.163 . . stop_ save_