data_5252 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural Differences in the NOE-derived Structure of G-T Mismatched DNA relative to Normal DNA are Correlated with Differences in (13)C Relaxation-based Internal Dynamics ; _BMRB_accession_number 5252 _BMRB_flat_file_name bmr5252.str _Entry_type new _Submission_date 2002-01-09 _Accession_date 2002-01-09 _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 Isaacs R. J. . 2 Rayens W. S. . 3 Spielmann H. P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-14 update BMRB 'update DNA residue label to two-letter code' 2002-09-10 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 5253 'd(CCATGCGTGG)2, G-T mismatch structure' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural Differences in the NOE-derived Structure of G-T Mismatched DNA relative to Normal DNA are Correlated with Differences in (13)C Relaxation-based Internal Dynamics ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22047884 _PubMed_ID 12051946 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Isaacs R. J. . 2 Rayens W. S. . 3 Spielmann H. P. . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_volume 319 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 191 _Page_last 207 _Year 2002 _Details . loop_ _Keyword 'G-T mismatch' dynamics 'spin relaxation' 'order parameter' 'helical parameter' 'sequence dependent structure' 'sequence dependent dynamics' stop_ save_ ################################## # Molecular system description # ################################## save_system_match_DNA _Saveframe_category molecular_system _Mol_system_name 5'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3' _Abbreviation_common CCACGCGTGG _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3' $match_DNA 5'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3' $match_DNA 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_match_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-3' _Abbreviation_common CCACGCGTGG _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence CCACGCGTGG loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DA 4 DC 5 DG 6 DC 7 DG 8 DT 9 DG 10 DG 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 $match_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 $match_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 $match_DNA 8 mL . NaCl 200 mM . NaPO4 20 mM . NaN3 10 mM . EDTA 0.1 mM . D2O 99.96 % . stop_ save_ ############################ # Computer software used # ############################ save_VNMR _Saveframe_category software _Name VNMR _Version 6b loop_ _Task collection stop_ _Details 'Varian, inc.' save_ save_FELIX _Saveframe_category software _Name FELIX _Version 98.0 loop_ _Task 'data analysis' stop_ _Details Accelrys. save_ save_MARDIGRAS _Saveframe_category software _Name MARDIGRAS _Version 1 loop_ _Task 'iterative matrix relaxation' stop_ _Details 'James, T.L.' save_ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 2.98 loop_ _Task 'structure solution' stop_ _Details Accelrys. 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 7.0 . n/a temperature 298 . K 'ionic strength' 0.230 . M pressure 1 . atm 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 . H 1 . ppm . . . . . . 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'-D(*CP*CP*AP*CP*GP*CP*GP*TP*GP*G)-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 DC H1' H 5.89 . . 2 . 1 DC H2'' H 2.03 . . 3 . 1 DC H4' H 4.09 . . 4 . 1 DC H2' H 2.48 . . 5 . 1 DC H3' H 4.64 . . 6 . 1 DC H5 H 5.84 . . 7 . 1 DC H6 H 7.69 . . 8 . 2 DC H1' H 5.35 . . 9 . 2 DC H2'' H 2.16 . . 10 . 2 DC H4' H 4.14 . . 11 . 2 DC H5'' H 4.05 . . 12 . 2 DC H2' H 2.41 . . 13 . 2 DC H3' H 4.87 . . 14 . 2 DC H5' H 4.00 . . 15 . 2 DC H5 H 5.72 . . 16 . 2 DC H6 H 7.61 . . 17 . 3 DA H1' H 6.27 . . 18 . 3 DA H2'' H 2.80 . . 19 . 3 DA H4' H 4.46 . . 20 . 3 DA H5'' H 4.46 . . 21 . 3 DA H2' H 2.93 . . 22 . 3 DA H3' H 5.08 . . 23 . 3 DA H5' H 4.05 . . 24 . 3 DA H2 H 7.87 . . 25 . 3 DA H8 H 8.33 . . 26 . 4 DC H1' H 5.58 . . 27 . 4 DC H2'' H 1.97 . . 28 . 4 DC H4' H 4.18 . . 29 . 4 DC H5'' H 4.18 . . 30 . 4 DC H2' H 2.35 . . 31 . 4 DC H3' H 4.84 . . 32 . 4 DC H5' H 4.28 . . 33 . 4 DC H5 H 5.32 . . 34 . 4 DC H6 H 7.26 . . 35 . 5 DG H1' H 5.88 . . 36 . 5 DG H2'' H 2.63 . . 37 . 5 DG H4' H 4.37 . . 38 . 5 DG H2' H 2.74 . . 39 . 5 DG H3' H 4.99 . . 40 . 5 DG H5' H 4.28 . . 41 . 5 DG H8 H 7.86 . . 42 . 6 DC H1' H 5.67 . . 43 . 6 DC H2'' H 2.03 . . 44 . 6 DC H4' H 4.18 . . 45 . 6 DC H2' H 2.40 . . 46 . 6 DC H3' H 4.85 . . 47 . 6 DC H5' H 4.20 . . 48 . 6 DC H5 H 5.34 . . 49 . 6 DC H6 H 7.30 . . 50 . 7 DG H1' H 5.96 . . 51 . 7 DG H2'' H 2.64 . . 52 . 7 DG H4' H 4.37 . . 53 . 7 DG H2' H 2.76 . . 54 . 7 DG H3' H 4.99 . . 55 . 7 DG H5' H 4.05 . . 56 . 7 DG H8 H 7.91 . . 57 . 8 DT H1' H 5.71 . . 58 . 8 DT H2'' H 1.89 . . 59 . 8 DT H4' H 4.15 . . 60 . 8 DT H5'' H 4.11 . . 61 . 8 DT H2' H 2.24 . . 62 . 8 DT H3' H 4.83 . . 63 . 8 DT H5' H 4.21 . . 64 . 8 DT H71 H 1.51 . . 65 . 8 DT H72 H 1.51 . . 66 . 8 DT H73 H 1.51 . . 67 . 8 DT H6 H 7.16 . . 68 . 9 DG H1' H 5.66 . . 69 . 9 DG H2'' H 2.66 . . 70 . 9 DG H4' H 4.36 . . 71 . 9 DG H5'' H 4.10 . . 72 . 9 DG H2' H 2.72 . . 73 . 9 DG H3' H 4.98 . . 74 . 9 DG H5' H 4.02 . . 75 . 9 DG H8 H 7.84 . . 76 . 10 DG H1' H 6.12 . . 77 . 10 DG H2'' H 2.54 . . 78 . 10 DG H4' H 4.23 . . 79 . 10 DG H2' H 2.39 . . 80 . 10 DG H3' H 4.67 . . 81 . 10 DG H5' H 4.23 . . 82 . 10 DG H8 H 7.78 . . stop_ save_