data_18907 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of Duplex DNA ; _BMRB_accession_number 18907 _BMRB_flat_file_name bmr18907.str _Entry_type original _Submission_date 2012-12-18 _Accession_date 2012-12-18 _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 Ghosh A. . . 2 Kar R. K. . 3 Jana J. . . 4 Biswas A. . . 5 Ghosh S. . . 6 Kumar D. . . 7 Chatterjee S. . . 8 Bhunia A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 225 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-01-11 original author . stop_ _Original_release_date 2013-01-11 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural Insights of DNA Duplex Stabilization by Potent Antimicrobial Peptide Indolicidin.' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ghosh A. . . 2 Kar R. K. . 3 Jana J. . . 4 Biswas A. . . 5 Ghosh S. . . 6 Kumar D. . . 7 Chatterjee S. . . 8 Bhunia A. . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Duplex DNA' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label GCGCATGCTACGCG $DNA_GCGCATGCTACGCG CGCGTAGCATGCGC $DNA_CGCGTAGCATGCGC stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_DNA_GCGCATGCTACGCG _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_GCGCATGCTACGCG _Molecular_mass 3952.606 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence GCGCATGCTACGCG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DC 5 DA 6 DT 7 DG 8 DC 9 DT 10 DA 11 DC 12 DG 13 DC 14 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_CGCGTAGCATGCGC _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_CGCGTAGCATGCGC _Molecular_mass 3952.606 _Mol_thiol_state 'not present' _Details . _Residue_count 14 _Mol_residue_sequence CGCGTAGCATGCGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 15 DC 2 16 DG 3 17 DC 4 18 DG 5 19 DT 6 20 DA 7 21 DG 8 22 DC 9 23 DA 10 24 DT 11 25 DG 12 26 DC 13 27 DG 14 28 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_GCGCATGCTACGCG . . . . Chemically "synthetic DNA" $DNA_CGCGTAGCATGCGC . . . . Chemically "synthetic DNA" 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_GCGCATGCTACGCG 'Chemically synthetic DNA' . Chemically "synthetic DNA" . . $DNA_CGCGTAGCATGCGC 'Chemically synthetic DNA' . Chemically "synthetic DNA" . . 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_GCGCATGCTACGCG 1 mM 'natural abundance' $DNA_CGCGTAGCATGCGC 1 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_AMBER _Saveframe_category software _Name AMBER _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 800 _Details 'Equipped with a cryoprobe' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7.2 . pH temperature 298 . 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 DSS H 1 'methyl protons' ppm 0.00 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_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H 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 GCGCATGCTACGCG _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 DG H1' H 6.18 0.003 . 2 1 1 DG H2' H 2.58 0.003 . 3 1 1 DG H2'' H 2.71 0.003 . 4 1 1 DG H3' H 4.95 0.003 . 5 1 1 DG H4' H 4.37 0.003 . 6 1 1 DG H8 H 7.74 0.005 . 7 2 2 DC H1' H 5.13 0.004 . 8 2 2 DC H2' H 2.42 0.004 . 9 2 2 DC H2'' H 3.24 0.004 . 10 2 2 DC H3' H 4.80 0.004 . 11 2 2 DC H4' H 4.11 0.004 . 12 2 2 DC H5 H 5.29 0.002 . 13 2 2 DC H6 H 7.24 0.004 . 14 2 2 DC H41 H 6.62 0.002 . 15 2 2 DC H42 H 6.42 0.003 . 16 3 3 DG H1 H 11.28 0.003 . 17 3 3 DG H1' H 5.99 0.002 . 18 3 3 DG H2' H 2.63 0.002 . 19 3 3 DG H2'' H 2.78 0.002 . 20 3 3 DG H3' H 4.99 0.002 . 21 3 3 DG H4' H 4.38 0.002 . 22 3 3 DG H8 H 7.83 0.004 . 23 4 4 DC H1' H 5.64 0.006 . 24 4 4 DC H2' H 1.96 0.006 . 25 4 4 DC H2'' H 2.11 0.006 . 26 4 4 DC H3' H 4.88 0.006 . 27 4 4 DC H4' H 4.16 0.006 . 28 4 4 DC H5 H 6.69 0.005 . 29 4 4 DC H6 H 7.42 0.003 . 30 4 4 DC H41 H 6.42 0.002 . 31 4 4 DC H42 H 10.2 0.004 . 32 5 5 DA H1' H 5.63 0.003 . 33 5 5 DA H2' H 2.66 0.005 . 34 5 5 DA H2'' H 2.99 0.002 . 35 5 5 DA H3' H 5.01 0.006 . 36 5 5 DA H4' H 4.41 0.005 . 37 5 5 DA H8 H 7.87 0.004 . 38 5 5 DA H61 H 6.28 0.006 . 39 5 5 DA H62 H 7.59 0.002 . 40 6 6 DT H1' H 5.5 0.005 . 41 6 6 DT H2' H 1.9 0.002 . 42 6 6 DT H2'' H 2.3 0.004 . 43 6 6 DT H3 H 11.9 0.003 . 44 6 6 DT H3' H 4.7 0.006 . 45 6 6 DT H4' H 4.2 0.008 . 46 6 6 DT H6 H 7.2 0.006 . 47 6 6 DT H71 H 1.3 0.007 . 48 6 6 DT H72 H 1.3 0.007 . 49 6 6 DT H73 H 1.3 0.007 . 50 7 7 DG H1 H 11.14 0.008 . 51 7 7 DG H1' H 5.7 0.004 . 52 7 7 DG H2' H 2.5 0.002 . 53 7 7 DG H2'' H 2.78 0.004 . 54 7 7 DG H3' H 5.0 0.003 . 55 7 7 DG H4' H 4.2 0.004 . 56 7 7 DG H8 H 7.9 0.006 . 57 8 8 DC H1' H 5.58 0.006 . 58 8 8 DC H2' H 1.81 0.004 . 59 8 8 DC H2'' H 2.24 0.005 . 60 8 8 DC H3' H 4.7 0.004 . 61 8 8 DC H4' H 4.20 0.005 . 62 8 8 DC H5 H 5.3 0.004 . 63 8 8 DC H6 H 7.24 0.007 . 64 8 8 DC H41 H 6.51 0.004 . 65 8 8 DC H42 H 10.2 0.005 . 66 9 9 DT H1' H 5.6 0.02 . 67 9 9 DT H2' H 1.8 0.03 . 68 9 9 DT H2'' H 2.9 0.04 . 69 9 9 DT H3 H 10.9 0.02 . 70 9 9 DT H3' H 5.0 0.05 . 71 9 9 DT H4' H 4.2 0.07 . 72 9 9 DT H6 H 7.4 0.06 . 73 9 9 DT H71 H 1.4 0.07 . 74 9 9 DT H72 H 1.4 0.07 . 75 9 9 DT H73 H 1.4 0.07 . 76 10 10 DA H1' H 5.73 0.003 . 77 10 10 DA H2' H 2.46 0.005 . 78 10 10 DA H2'' H 2.92 0.002 . 79 10 10 DA H3' H 5.11 0.006 . 80 10 10 DA H4' H 4.54 0.005 . 81 10 10 DA H8 H 7.57 0.004 . 82 10 10 DA H61 H 6.34 0.006 . 83 10 10 DA H62 H 7.42 0.002 . 84 11 11 DC H1' H 5.58 0.006 . 85 11 11 DC H2' H 1.81 0.004 . 86 11 11 DC H2'' H 2.24 0.005 . 87 11 11 DC H3' H 4.7 0.004 . 88 11 11 DC H4' H 4.20 0.005 . 89 11 11 DC H5 H 5.3 0.004 . 90 11 11 DC H6 H 7.24 0.007 . 91 11 11 DC H41 H 6.55 0.004 . 92 11 11 DC H42 H 10.2 0.005 . 93 12 12 DG H1 H 11.44 0.008 . 94 12 12 DG H1' H 5.8 0.004 . 95 12 12 DG H2' H 2.3 0.002 . 96 12 12 DG H2'' H 2.88 0.004 . 97 12 12 DG H3' H 5.15 0.003 . 98 12 12 DG H4' H 4.4 0.004 . 99 12 12 DG H8 H 7.87 0.006 . 100 13 13 DC H1' H 5.78 0.006 . 101 13 13 DC H2' H 1.91 0.004 . 102 13 13 DC H2'' H 2.34 0.005 . 103 13 13 DC H3' H 4.74 0.004 . 104 13 13 DC H4' H 4.40 0.005 . 105 13 13 DC H5 H 5.30 0.004 . 106 13 13 DC H6 H 7.44 0.007 . 107 13 13 DC H41 H 6.58 0.004 . 108 13 13 DC H42 H 10.34 0.005 . 109 14 14 DG H1 H 10.14 0.008 . 110 14 14 DG H1' H 5.6 0.004 . 111 14 14 DG H2' H 2.34 0.002 . 112 14 14 DG H2'' H 2.98 0.004 . 113 14 14 DG H3' H 4.97 0.003 . 114 14 14 DG H4' H 4.14 0.004 . 115 14 14 DG H8 H 7.46 0.006 . stop_ save_ save_assigned_chem_shift_list_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H 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 CGCGTAGCATGCGC _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 15 1 DC H1' H 5.74 0.007 . 2 15 1 DC H2' H 1.74 0.001 . 3 15 1 DC H2'' H 2.44 0.003 . 4 15 1 DC H3' H 4.74 0.002 . 5 15 1 DC H4' H 4.14 0.005 . 6 15 1 DC H6 H 7.54 0.004 . 7 16 2 DG H1 H 11.45 0.003 . 8 16 2 DG H1' H 5.89 0.002 . 9 16 2 DG H2' H 2.57 0.002 . 10 16 2 DG H2'' H 2.69 0.002 . 11 16 2 DG H3' H 4.45 0.002 . 12 16 2 DG H4' H 4.34 0.002 . 13 16 2 DG H8 H 7.73 0.004 . 14 17 3 DC H1' H 5.45 0.006 . 15 17 3 DC H2' H 1.94 0.006 . 16 17 3 DC H2'' H 2.15 0.006 . 17 17 3 DC H3' H 4.94 0.006 . 18 17 3 DC H4' H 4.22 0.006 . 19 17 3 DC H5 H 6.58 0.005 . 20 17 3 DC H6 H 7.47 0.003 . 21 17 3 DC H41 H 6.42 0.002 . 22 17 3 DC H42 H 10.25 0.004 . 23 18 4 DG H1 H 11.48 0.003 . 24 18 4 DG H1' H 5.97 0.002 . 25 18 4 DG H2' H 2.54 0.002 . 26 18 4 DG H2'' H 2.69 0.002 . 27 18 4 DG H3' H 4.94 0.002 . 28 18 4 DG H4' H 4.44 0.002 . 29 18 4 DG H8 H 7.73 0.004 . 30 19 5 DT H1' H 5.67 0.02 . 31 19 5 DT H2' H 1.98 0.003 . 32 19 5 DT H2'' H 2.78 0.04 . 33 19 5 DT H3 H 10.7 0.02 . 34 19 5 DT H3' H 5.11 0.05 . 35 19 5 DT H4' H 4.12 0.07 . 36 19 5 DT H6 H 7.5 0.06 . 37 19 5 DT H71 H 1.52 0.07 . 38 19 5 DT H72 H 1.52 0.07 . 39 19 5 DT H73 H 1.52 0.07 . 40 20 6 DA H1' H 5.83 0.003 . 41 20 6 DA H2' H 2.26 0.005 . 42 20 6 DA H2'' H 2.82 0.002 . 43 20 6 DA H3' H 5.31 0.006 . 44 20 6 DA H4' H 4.64 0.005 . 45 20 6 DA H8 H 7.37 0.004 . 46 20 6 DA H61 H 13.40 0.006 . 47 20 6 DA H62 H 12.10 0.002 . 48 21 7 DG H1 H 11.44 0.008 . 49 21 7 DG H1' H 5.8 0.004 . 50 21 7 DG H2' H 2.3 0.002 . 51 21 7 DG H2'' H 2.88 0.004 . 52 21 7 DG H3' H 5.15 0.003 . 53 21 7 DG H4' H 4.4 0.004 . 54 21 7 DG H8 H 7.87 0.006 . 55 22 8 DC H1' H 5.43 0.004 . 56 22 8 DC H2' H 2.32 0.004 . 57 22 8 DC H2'' H 3.14 0.004 . 58 22 8 DC H3' H 4.90 0.004 . 59 22 8 DC H4' H 4.21 0.004 . 60 22 8 DC H5 H 5.19 0.002 . 61 22 8 DC H6 H 7.44 0.004 . 62 22 8 DC H41 H 12.08 0.002 . 63 22 8 DC H42 H 10.48 0.003 . 64 23 9 DA H1' H 5.73 0.003 . 65 23 9 DA H2' H 2.76 0.005 . 66 23 9 DA H2'' H 3.00 0.002 . 67 23 9 DA H3' H 5.10 0.006 . 68 23 9 DA H4' H 4.31 0.005 . 69 23 9 DA H8 H 7.87 0.004 . 70 23 9 DA H61 H 12.47 0.006 . 71 23 9 DA H62 H 12.90 0.002 . 72 24 10 DT H1' H 5.64 0.02 . 73 24 10 DT H2' H 1.86 0.03 . 74 24 10 DT H2'' H 2.85 0.04 . 75 24 10 DT H3 H 10.8 0.02 . 76 24 10 DT H3' H 5.10 0.05 . 77 24 10 DT H4' H 4.24 0.07 . 78 24 10 DT H6 H 7.6 0.06 . 79 24 10 DT H71 H 1.35 0.07 . 80 24 10 DT H72 H 1.35 0.07 . 81 24 10 DT H73 H 1.35 0.07 . 82 25 11 DG H1 H 10.84 0.008 . 83 25 11 DG H1' H 5.75 0.004 . 84 25 11 DG H2' H 2.41 0.002 . 85 25 11 DG H2'' H 2.95 0.004 . 86 25 11 DG H3' H 5.10 0.003 . 87 25 11 DG H4' H 4.45 0.004 . 88 25 11 DG H8 H 7.67 0.006 . 89 26 12 DC H1' H 5.43 0.004 . 90 26 12 DC H2' H 2.32 0.004 . 91 26 12 DC H2'' H 3.34 0.004 . 92 26 12 DC H3' H 4.90 0.004 . 93 26 12 DC H4' H 4.21 0.004 . 94 26 12 DC H5 H 5.39 0.002 . 95 26 12 DC H6 H 7.34 0.004 . 96 26 12 DC H41 H 6.58 0.002 . 97 27 13 DG H1 H 11.54 0.008 . 98 27 13 DG H1' H 5.8 0.004 . 99 27 13 DG H2' H 2.35 0.002 . 100 27 13 DG H2'' H 2.78 0.004 . 101 27 13 DG H3' H 5.20 0.003 . 102 27 13 DG H4' H 4.52 0.004 . 103 27 13 DG H8 H 7.77 0.006 . 104 28 14 DC H1' H 5.51 0.006 . 105 28 14 DC H2' H 1.80 0.004 . 106 28 14 DC H2'' H 2.34 0.005 . 107 28 14 DC H3' H 4.75 0.004 . 108 28 14 DC H4' H 4.30 0.005 . 109 28 14 DC H5 H 5.31 0.004 . 110 28 14 DC H6 H 7.35 0.007 . stop_ save_