data_5164 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of a Parallel Stranded DNA Duplex at Atomic Resolution ; _BMRB_accession_number 5164 _BMRB_flat_file_name bmr5164.str _Entry_type new _Submission_date 2001-10-03 _Accession_date 2001-10-03 _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 Parvathy V. R. . 2 Bhaumik S. R. . 3 Chary K. V. . 4 Govil G. . . 5 Liu K. . . 6 Howard F. W. . 7 Miles H. T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 232 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-16 update BMRB 'update DNA residue label to two-letter code' 2002-08-23 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR Structure of a Parallel-stranded DNA Duplex at Atomic Resolution' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 21914663 _PubMed_ID 11917010 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Parvathy V. R. . 2 Bhaumik S. R. . 3 Chary K. V. . 4 Govil G. . . 5 Liu K. . . 6 Howard F. W. . 7 Miles H. T. . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume 30 _Journal_issue 7 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1500 _Page_last 1511 _Year 2002 _Details . loop_ _Keyword 'Parallel stranded' 'DNA duplex' stop_ save_ ################################## # Molecular system description # ################################## save_system_DNA _Saveframe_category molecular_system _Mol_system_name "5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3' duplex" _Abbreviation_common 'DNA duplex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3' $DNA_s1 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3' $DNA_s2 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state dimeric _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_s1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*CP*C)-3' _Abbreviation_common DNA_s1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence CCATAATTTACC loop_ _Residue_seq_code _Residue_label 1 DC 2 DC 3 DA 4 DT 5 DA 6 DA 7 DT 8 DT 9 DT 10 DA 11 DC 12 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_s2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 5'-D(P*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*CP*C)-3' _Abbreviation_common DNA_s2 _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence CCTAAATTATCC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 DC 2 14 DC 3 15 DT 4 16 DA 5 17 DA 6 18 DA 7 19 DT 8 20 DT 9 21 DA 10 22 DT 11 23 DC 12 24 DC 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 $DNA_s1 . . . . . . $DNA_s2 . . . . . . 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 $DNA_s1 . . . . . . $DNA_s2 . . . . . . 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 $DNA_s1 5 mM . $DNA_s2 5 mM . 'sodium acetate buffer' 0.05 M [U-2H] NaCl 0.1 M . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_DISCOVER _Saveframe_category software _Name DISCOVER _Version 3.1 loop_ _Task 'structure solution' refinement stop_ _Details MSI save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UNITY _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _Sample_label . save_ save_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _Sample_label . save_ save_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name COSY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _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 5.5 . n/a temperature 303 . K 'ionic strength' 0.15 . 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(P*CP*CP*AP*TP*AP*AP*TP*TP*TP*AP*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 DC H5 H 6.13 0.01 1 2 . 1 DC H6 H 7.67 0.01 1 3 . 1 DC H1' H 5.89 0.01 1 4 . 1 DC H2' H 2.54 0.01 1 5 . 1 DC H2'' H 2.67 0.01 1 6 . 1 DC H3' H 5.02 0.01 1 7 . 1 DC H4' H 4.39 0.01 1 8 . 1 DC H5' H 4.14 0.01 2 9 . 1 DC H5'' H 4.14 0.01 2 10 . 2 DC H5 H 5.98 0.01 1 11 . 2 DC H6 H 7.63 0.01 1 12 . 2 DC H1' H 5.97 0.01 1 13 . 2 DC H2' H 1.91 0.01 1 14 . 2 DC H2'' H 2.36 0.01 1 15 . 2 DC H3' H 5.04 0.01 1 16 . 2 DC H4' H 4.41 0.01 1 17 . 2 DC H5' H 4.41 0.01 2 18 . 2 DC H5'' H 4.06 0.01 2 19 . 3 DA H2 H 7.49 0.01 1 20 . 3 DA H8 H 8.36 0.01 1 21 . 3 DA H1' H 6.29 0.01 1 22 . 3 DA H2' H 2.72 0.01 1 23 . 3 DA H2'' H 2.83 0.01 1 24 . 3 DA H3' H 4.79 0.01 1 25 . 3 DA H4' H 4.36 0.01 1 26 . 3 DA H5' H 4.17 0.01 2 27 . 3 DA H5'' H 4.13 0.01 2 28 . 4 DT H3 H 13.65 0.01 1 29 . 4 DT H6 H 7.2 0.01 1 30 . 4 DT H71 H 1.69 0.01 1 31 . 4 DT H72 H 1.69 0.01 1 32 . 4 DT H73 H 1.69 0.01 1 33 . 4 DT H1' H 5.79 0.01 1 34 . 4 DT H2' H 2.78 0.01 1 35 . 4 DT H2'' H 2.12 0.01 1 36 . 4 DT H3' H 5 0.01 1 37 . 4 DT H4' H 4.26 0.01 1 38 . 4 DT H5' H 3.9 0.01 2 39 . 4 DT H5'' H 3.84 0.01 2 40 . 5 DA H8 H 8.16 0.01 1 41 . 5 DA H1' H 6.35 0.01 1 42 . 5 DA H2' H 2.62 0.01 1 43 . 5 DA H2'' H 2.7 0.01 1 44 . 5 DA H3' H 5.07 0.01 1 45 . 5 DA H4' H 4.37 0.01 1 46 . 5 DA H5' H 4.01 0.01 2 47 . 5 DA H5'' H 4.08 0.01 2 48 . 6 DA H2 H 7.41 0.01 1 49 . 6 DA H8 H 8.31 0.01 1 50 . 6 DA H1' H 6.27 0.01 1 51 . 6 DA H2' H 2.72 0.01 1 52 . 6 DA H2'' H 2.8 0.01 1 53 . 6 DA H3' H 4.85 0.01 1 54 . 6 DA H4' H 4.44 0.01 1 55 . 6 DA H5' H 4.29 0.01 2 56 . 6 DA H5'' H 4.2 0.01 2 57 . 7 DT H3 H 13.93 0.01 1 58 . 7 DT H6 H 7.37 0.01 1 59 . 7 DT H71 H 1.67 0.01 1 60 . 7 DT H72 H 1.67 0.01 1 61 . 7 DT H73 H 1.67 0.01 1 62 . 7 DT H1' H 6.04 0.01 1 63 . 7 DT H2' H 2.19 0.01 1 64 . 7 DT H2'' H 2.47 0.01 1 65 . 7 DT H3' H 4.91 0.01 1 66 . 7 DT H4' H 4.26 0.01 1 67 . 7 DT H5' H 4.1 0.01 2 68 . 7 DT H5'' H 4.1 0.01 2 69 . 8 DT H3 H 13.97 0.01 1 70 . 8 DT H6 H 7.51 0.01 1 71 . 8 DT H71 H 1.79 0.01 1 72 . 8 DT H72 H 1.79 0.01 1 73 . 8 DT H73 H 1.79 0.01 1 74 . 8 DT H1' H 6.11 0.01 1 75 . 8 DT H2' H 2.19 0.01 1 76 . 8 DT H2'' H 2.47 0.01 1 77 . 8 DT H3' H 4.88 0.01 1 78 . 8 DT H4' H 4.32 0.01 1 79 . 8 DT H5' H 4.23 0.01 2 80 . 8 DT H5'' H 4.16 0.01 2 81 . 9 DT H3 H 13.73 0.01 1 82 . 9 DT H6 H 7.37 0.01 1 83 . 9 DT H71 H 1.83 0.01 1 84 . 9 DT H72 H 1.83 0.01 1 85 . 9 DT H73 H 1.83 0.01 1 86 . 9 DT H1' H 5.95 0.01 1 87 . 9 DT H2' H 1.88 0.01 1 88 . 9 DT H2'' H 2.3 0.01 1 89 . 9 DT H3' H 4.84 0.01 1 90 . 9 DT H4' H 4.35 0.01 1 91 . 9 DT H5' H 4.17 0.01 2 92 . 9 DT H5'' H 4.17 0.01 2 93 . 10 DA H2 H 7.22 0.01 1 94 . 10 DA H8 H 8.36 0.01 1 95 . 10 DA H1' H 6.34 0.01 1 96 . 10 DA H2' H 2.79 0.01 1 97 . 10 DA H2'' H 2.89 0.01 1 98 . 10 DA H3' H 4.84 0.01 1 99 . 10 DA H4' H 4.62 0.01 1 100 . 10 DA H5' H 4.21 0.01 2 101 . 10 DA H5'' H 4.16 0.01 2 102 . 11 DC H5 H 6.04 0.01 1 103 . 11 DC H6 H 7.67 0.01 1 104 . 11 DC H1' H 6.2 0.01 1 105 . 11 DC H2' H 2.25 0.01 1 106 . 11 DC H2'' H 2.53 0.01 1 107 . 11 DC H3' H 4.83 0.01 1 108 . 11 DC H4' H 4.19 0.01 1 109 . 11 DC H5' H 3.84 0.01 2 110 . 11 DC H5'' H 3.77 0.01 2 111 . 12 DC H5 H 6.06 0.01 1 112 . 12 DC H6 H 7.87 0.01 1 113 . 12 DC H1' H 5.98 0.01 1 114 . 12 DC H2' H 1.9 0.01 1 115 . 12 DC H2'' H 1.9 0.01 1 116 . 12 DC H3' H 4.81 0.01 1 117 . 12 DC H4' H 4.19 0.01 1 118 . 12 DC H5' H 3.97 0.01 2 119 . 12 DC H5'' H 3.97 0.01 2 stop_ save_ save_chemical_shift_set_2 _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*CP*CP*TP*AP*TP*TP*AP*AP*AP*TP*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 DC H5 H 6.07 0.01 1 2 . 1 DC H6 H 7.88 0.01 1 3 . 1 DC H1' H 6.07 0.01 1 4 . 1 DC H2' H 2.29 0.01 1 5 . 1 DC H3' H 4.56 0.01 1 6 . 1 DC H5' H 4.1 0.01 2 7 . 1 DC H5'' H 4.15 0.01 2 8 . 2 DC H5 H 6.03 0.01 1 9 . 2 DC H6 H 7.77 0.01 1 10 . 2 DC H1' H 6.28 0.01 1 11 . 2 DC H2' H 2.26 0.01 1 12 . 2 DC H2'' H 2.51 0.01 1 13 . 2 DC H3' H 4.91 0.01 1 14 . 2 DC H5' H 4.2 0.01 2 15 . 2 DC H5'' H 4.2 0.01 2 16 . 3 DT H3 H 13.41 0.01 1 17 . 3 DT H6 H 7.29 0.01 1 18 . 3 DT H71 H 1.64 0.01 1 19 . 3 DT H72 H 1.64 0.01 1 20 . 3 DT H73 H 1.64 0.01 1 21 . 3 DT H1' H 5.82 0.01 1 22 . 3 DT H2' H 2.12 0.01 1 23 . 3 DT H2'' H 2.39 0.01 1 24 . 3 DT H3' H 4.84 0.01 1 25 . 3 DT H4' H 4.1 0.01 1 26 . 3 DT H5' H 4.1 0.01 2 27 . 3 DT H5'' H 4.1 0.01 2 28 . 4 DA H8 H 8.26 0.01 1 29 . 4 DA H1' H 6.2 0.01 1 30 . 4 DA H2' H 2.7 0.01 1 31 . 4 DA H2'' H 2.77 0.01 1 32 . 4 DA H3' H 5.05 0.01 1 33 . 4 DA H4' H 4.47 0.01 1 34 . 4 DA H5' H 4.15 0.01 2 35 . 4 DA H5'' H 4.15 0.01 2 36 . 5 DA H2 H 7.85 0.01 1 37 . 5 DA H8 H 8.14 0.01 1 38 . 5 DA H1' H 5.86 0.01 1 39 . 5 DA H2' H 2.59 0.01 1 40 . 5 DA H2'' H 2.71 0.01 1 41 . 5 DA H3' H 4.83 0.01 1 42 . 5 DA H4' H 4.25 0.01 1 43 . 5 DA H5' H 4.06 0.01 2 44 . 5 DA H5'' H 4.06 0.01 2 45 . 6 DA H2 H 7.12 0.01 1 46 . 6 DA H8 H 8.18 0.01 1 47 . 6 DA H1' H 5.9 0.01 1 48 . 6 DA H2' H 2.62 0.01 1 49 . 6 DA H2'' H 2.72 0.01 1 50 . 6 DA H3' H 4.79 0.01 1 51 . 6 DA H4' H 4.26 0.01 1 52 . 6 DA H5' H 3.89 0.01 2 53 . 6 DA H5'' H 3.84 0.01 2 54 . 7 DT H3 H 13.67 0.01 1 55 . 7 DT H6 H 7.28 0.01 1 56 . 7 DT H71 H 1.8 0.01 1 57 . 7 DT H72 H 1.8 0.01 1 58 . 7 DT H73 H 1.8 0.01 1 59 . 7 DT H1' H 5.85 0.01 1 60 . 7 DT H2' H 1.73 0.01 1 61 . 7 DT H2'' H 2.13 0.01 1 62 . 7 DT H3' H 4.78 0.01 1 63 . 7 DT H4' H 4.22 0.01 1 64 . 7 DT H5' H 4.15 0.01 2 65 . 7 DT H5'' H 4.15 0.01 2 66 . 8 DT H3 H 13.38 0.01 1 67 . 8 DT H6 H 7.42 0.01 1 68 . 8 DT H71 H 1.71 0.01 1 69 . 8 DT H72 H 1.71 0.01 1 70 . 8 DT H73 H 1.71 0.01 1 71 . 8 DT H1' H 6.08 0.01 1 72 . 8 DT H2' H 2.18 0.01 1 73 . 8 DT H2'' H 2.45 0.01 1 74 . 8 DT H3' H 4.87 0.01 1 75 . 8 DT H4' H 4.25 0.01 1 76 . 8 DT H5' H 4.1 0.01 2 77 . 8 DT H5'' H 4.1 0.01 2 78 . 9 DA H2 H 8.39 0.01 1 79 . 9 DA H8 H 8.41 0.01 1 80 . 9 DA H1' H 6.36 0.01 1 81 . 9 DA H2' H 2.83 0.01 1 82 . 9 DA H2'' H 2.89 0.01 1 83 . 9 DA H3' H 5.06 0.01 1 84 . 9 DA H4' H 4.47 0.01 1 85 . 9 DA H5' H 4.17 0.01 2 86 . 9 DA H5'' H 4.15 0.01 2 87 . 10 DT H3 H 14.21 0.01 1 88 . 10 DT H6 H 7.44 0.01 1 89 . 10 DT H71 H 1.88 0.01 1 90 . 10 DT H72 H 1.88 0.01 1 91 . 10 DT H73 H 1.88 0.01 1 92 . 10 DT H1' H 5.96 0.01 1 93 . 10 DT H2' H 1.97 0.01 1 94 . 10 DT H2'' H 2.36 0.01 1 95 . 10 DT H3' H 4.84 0.01 1 96 . 10 DT H4' H 4.21 0.01 1 97 . 10 DT H5' H 3.86 0.01 2 98 . 10 DT H5'' H 3.81 0.01 2 99 . 11 DC H5 H 6.01 0.01 1 100 . 11 DC H6 H 7.82 0.01 1 101 . 11 DC H1' H 6.1 0.01 1 102 . 11 DC H2' H 2.23 0.01 1 103 . 11 DC H2'' H 2.55 0.01 1 104 . 11 DC H3' H 4.91 0.01 1 105 . 11 DC H4' H 4.34 0.01 1 106 . 11 DC H5' H 4.17 0.01 2 107 . 11 DC H5'' H 4.17 0.01 2 108 . 12 DC H5 H 5.97 0.01 1 109 . 12 DC H6 H 7.72 0.01 1 110 . 12 DC H1' H 6.14 0.01 1 111 . 12 DC H2' H 2.21 0.01 1 112 . 12 DC H2'' H 2.51 0.01 1 113 . 12 DC H3' H 4.92 0.01 1 stop_ save_