data_6186 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spec and restrained molecular dynamics ; _BMRB_accession_number 6186 _BMRB_flat_file_name bmr6186.str _Entry_type new _Submission_date 2004-04-22 _Accession_date 2004-04-22 _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 Barthwal R. . . 2 Awasthi P. . . 3 Narang M. . . 4 Sharma U. . . 5 Srivastava N. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 47 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2004-11-08 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structure of DNA sequence d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy and restrained molecular dynamics ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15363786 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Barthwal R. . . 2 Awasthi P. . . 3 Monica . . . 4 Kaur M. . . 5 Sharma U. . . 6 Srivastava N. . . 7 Barthwal S. K. . 8 Govil G. . . stop_ _Journal_abbreviation 'J. Struct. Biol.' _Journal_volume 148 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 34 _Page_last 50 _Year 2004 _Details . loop_ _Keyword 'TpG/CpA BASEPAIR STEP' '2D-NMR OF d-TGATCA' 'RESTRAINED MOLECULAR DYNAMICS' 'SEQUENCE RELATED CONFORMATION' 'DNA FLEXIBILITY' stop_ save_ ################################## # Molecular system description # ################################## save_system_TGATCA _Saveframe_category molecular_system _Mol_system_name 5'-D(P*TP*GP*AP*TP*CP*A)-3' _Abbreviation_common 5'-D(P*TP*GP*AP*TP*CP*A)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label '5'-D(P*TP*GP*AP*TP*CP*A)-3', chain 1' $TGATCA '5'-D(P*TP*GP*AP*TP*CP*A)-3', chain 2' $TGATCA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_TGATCA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common TGATCA _Abbreviation_common TGATCA _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 6 _Mol_residue_sequence TGATCA loop_ _Residue_seq_code _Residue_label 1 DT 2 DG 3 DA 4 DT 5 DC 6 DA 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 $TGATCA . . . . . . 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 $TGATCA '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 $TGATCA 7.36 mM . 'phosphate buffer' 20 mM . NaCl 15 mM . D2O 100 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $TGATCA 9.14 mM . 'phosphate buffer' 20 mM . NaCl 15 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 97 loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AM _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_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _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 295 . K 'ionic strength' 35 . mM 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 _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 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(P*TP*GP*AP*TP*CP*A)-3', chain 1' _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 DT H1' H 5.90 0.01 1 2 . 1 DT H2' H 1.76 0.01 1 3 . 1 DT H2'' H 2.25 0.01 1 4 . 1 DT H3' H 4.65 0.01 1 5 . 1 DT H4' H 4.07 0.01 1 6 . 1 DT H5' H 4.35 0.01 1 7 . 1 DT H5'' H 3.61 0.01 1 8 . 2 DG H1' H 5.57 0.01 1 9 . 2 DG H2' H 2.79 0.01 1 10 . 2 DG H2'' H 2.84 0.01 1 11 . 2 DG H3' H 5.06 0.01 1 12 . 2 DG H4' H 4.35 0.01 1 13 . 2 DG H5' H 4.07 0.01 1 14 . 2 DG H5'' H 3.98 0.01 1 15 . 3 DA H8 H 8.02 0.01 1 16 . 3 DA H1' H 6.34 0.01 1 17 . 3 DA H2' H 2.76 0.01 1 18 . 3 DA H2'' H 2.96 0.01 1 19 . 3 DA H3' H 5.06 0.01 1 20 . 3 DA H4' H 4.52 0.01 1 21 . 3 DA H5' H 4.31 0.01 1 22 . 3 DA H5'' H 4.22 0.01 1 23 . 4 DT H6 H 8.33 0.01 1 24 . 4 DT H1' H 6.04 0.01 1 25 . 4 DT H2' H 2.02 0.01 1 26 . 4 DT H2'' H 2.39 0.01 1 27 . 4 DT H3' H 4.86 0.01 1 28 . 4 DT H4' H 4.20 0.01 1 29 . 4 DT H5' H 4.19 0.01 1 30 . 4 DT H5'' H 4.18 0.01 1 31 . 5 DC H5 H 5.80 0.01 1 32 . 5 DC H6 H 7.52 0.01 1 33 . 5 DC H1' H 5.90 0.01 1 34 . 5 DC H2' H 1.99 0.01 1 35 . 5 DC H2'' H 2.30 0.01 1 36 . 5 DC H3' H 4.80 0.01 1 37 . 5 DC H4' H 4.02 0.01 1 38 . 5 DC H5' H 3.97 0.01 1 39 . 5 DC H5'' H 3.95 0.01 1 40 . 6 DA H8 H 8.28 0.01 1 41 . 6 DA H1' H 6.34 0.01 1 42 . 6 DA H2' H 2.76 0.01 1 43 . 6 DA H2'' H 2.53 0.01 1 44 . 6 DA H3' H 4.74 0.01 1 45 . 6 DA H4' H 4.23 0.01 1 46 . 6 DA H5' H 4.10 0.01 1 47 . 6 DA H5'' H 4.06 0.01 1 stop_ save_