data_30053 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of PT-free dsDNA from Streptomyces lividans ; _BMRB_accession_number 30053 _BMRB_flat_file_name bmr30053.str _Entry_type original _Submission_date 2016-03-30 _Accession_date 2016-03-30 _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 Lan Wenxian . . 2 Cao Chunyang . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 156 "31P chemical shifts" 16 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-11-15 update BMRB 'update entry citation' 2016-06-20 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30052 '[Rp, Rp]-PT dsDNA' 30054 '[Sp, Sp]-PT dsDNA' stop_ _Original_release_date 2016-06-20 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural investigation into physiological DNA phosphorothioate modification ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27169778 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lan Wenxian . . 2 Hu Zhongpei . . 3 Cao Chunyang . . stop_ _Journal_abbreviation 'Sci. Rep.' _Journal_volume 6 _Journal_issue . _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 25737 _Page_last 25737 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3'), DNA (5'-D(*TP*CP*GP*GP*CP*GP*GP*CP*CP*G)-3')" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 entity_2 $entity_2 stop_ _System_molecular_weight . _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common "DNA (5'-D(*CP*GP*GP*CP*CP*GP*CP*CP*GP*A)-3')" _Molecular_mass 3030.981 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; CGGCCGCCGA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DG 4 4 DC 5 5 DC 6 6 DG 7 7 DC 8 8 DC 9 9 DG 10 10 DA stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common "DNA (5'-D(*TP*CP*GP*GP*CP*GP*GP*CP*CP*G)-3')" _Molecular_mass 3061.992 _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence ; TCGGCGGCCG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 11 DT 2 12 DC 3 13 DG 4 14 DG 5 15 DC 6 16 DG 7 17 DG 8 18 DC 9 19 DC 10 20 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 $entity_1 'high GC Gram+' 1916 Bacteria . Streptomyces lividans $entity_2 'high GC Gram+' 1916 Bacteria . Streptomyces lividans 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 $entity_1 'recombinant technology' . Streptomyces lividans . . $entity_2 'recombinant technology' . Streptomyces lividans . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1.0 mM PT-free dsDNA, 100 mM NaCl, 40 mM NaPO4, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling NaCl 100 mM 'natural abundance' NaPO4 40 mM 'natural abundance' $entity_1 1.0 mM none H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name NMRDraw _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DD2 _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DD2 _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_2D_1H-31P_hetcor_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P hetcor' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 360 0.1 mM pH 7.0 0.002 pH pressure 1.0 0.001 atm temperature 298 0.1 K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 360 0.1 mM pH 7.0 0.01 pH pressure 1 0.0001 atm temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_2 stop_ loop_ _Experiment_label '2D NOESY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_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 1 DC H1' H 5.769 . . 2 1 1 DC H2' H 1.871 . . 3 1 1 DC H2'' H 2.365 . . 4 1 1 DC H3' H 4.707 . . 5 1 1 DC H4' H 4.072 . . 6 1 1 DC H5 H 5.918 . . 7 1 1 DC H5'' H 3.72 . . 8 1 1 DC H6 H 7.608 . . 9 2 2 DG H1' H 5.569 . . 10 2 2 DG H2' H 2.737 . . 11 2 2 DG H2'' H 2.773 . . 12 2 2 DG H3' H 5.004 . . 13 2 2 DG H4' H 4.333 . . 14 2 2 DG H8 H 7.936 . . 15 2 2 DG P P 3.734 . . 16 3 3 DG H1' H 5.963 . . 17 3 3 DG H2' H 2.63 . . 18 3 3 DG H2'' H 2.736 . . 19 3 3 DG H3' H 5.023 . . 20 3 3 DG H4' H 4.448 . . 21 3 3 DG H5' H 4.179 . . 22 3 3 DG H5'' H 4.21 . . 23 3 3 DG H8 H 7.825 . . 24 3 3 DG P P 3.843 . . 25 4 4 DC H1' H 5.976 . . 26 4 4 DC H2' H 2.086 . . 27 4 4 DC H2'' H 2.477 . . 28 4 4 DC H3' H 4.861 . . 29 4 4 DC H4' H 4.239 . . 30 4 4 DC H5 H 5.311 . . 31 4 4 DC H6 H 7.365 . . 32 4 4 DC H41 H 6.354 . . 33 4 4 DC H42 H 8.159 . . 34 4 4 DC P P 3.586 . . 35 5 5 DC H1' H 5.582 . . 36 5 5 DC H2' H 2.038 . . 37 5 5 DC H2'' H 2.389 . . 38 5 5 DC H3' H 4.831 . . 39 5 5 DC H4' H 4.11 . . 40 5 5 DC H5 H 5.559 . . 41 5 5 DC H6 H 7.419 . . 42 5 5 DC H41 H 6.745 . . 43 5 5 DC H42 H 8.539 . . 44 5 5 DC P P 3.609 . . 45 6 6 DG H1' H 5.914 . . 46 6 6 DG H2' H 2.578 . . 47 6 6 DG H2'' H 2.737 . . 48 6 6 DG H3' H 5.004 . . 49 6 6 DG H4' H 4.349 . . 50 6 6 DG H8 H 7.921 . . 51 6 6 DG P P 3.634 . . 52 7 7 DC H2' H 2.026 . . 53 7 7 DC H2'' H 2.458 . . 54 7 7 DC H3' H 4.832 . . 55 7 7 DC H4' H 4.198 . . 56 7 7 DC H5 H 5.372 . . 57 7 7 DC H6 H 7.368 . . 58 7 7 DC H41 H 6.37 . . 59 7 7 DC P P 3.621 . . 60 8 8 DC H1' H 5.49 . . 61 8 8 DC H2' H 1.837 . . 62 8 8 DC H2'' H 2.211 . . 63 8 8 DC H3' H 4.806 . . 64 8 8 DC H4' H 4.044 . . 65 8 8 DC H5 H 5.634 . . 66 8 8 DC H5'' H 3.952 . . 67 8 8 DC H6 H 7.395 . . 68 8 8 DC H41 H 6.892 . . 69 8 8 DC H42 H 8.68 . . 70 8 8 DC P P 3.623 . . 71 9 9 DG H1' H 5.702 . . 72 9 9 DG H2' H 2.601 . . 73 9 9 DG H2'' H 2.655 . . 74 9 9 DG H3' H 4.967 . . 75 9 9 DG H4' H 4.288 . . 76 9 9 DG H5' H 3.948 . . 77 9 9 DG H5'' H 4.044 . . 78 9 9 DG H8 H 7.848 . . 79 9 9 DG P P 3.859 . . 80 10 10 DA H1' H 6.494 . . 81 10 10 DA H2 H 6.342 . . 82 10 10 DA H2' H 2.55 . . 83 10 10 DA H2'' H 2.452 . . 84 10 10 DA H3' H 4.709 . . 85 10 10 DA H4' H 4.231 . . 86 10 10 DA H8 H 8.193 . . 87 10 10 DA P P 3.761 . . stop_ save_ save_assigned_chemical_shifts_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_2 stop_ loop_ _Experiment_label '2D NOESY' '2D 1H-1H TOCSY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name entity_2 _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 11 1 DT H1' H 6.093 . . 2 11 1 DT H2' H 2.123 . . 3 11 1 DT H2'' H 2.495 . . 4 11 1 DT H3' H 4.721 . . 5 11 1 DT H4' H 4.135 . . 6 11 1 DT H5'' H 3.724 . . 7 11 1 DT H6 H 7.519 . . 8 12 2 DC H1' H 5.609 . . 9 12 2 DC H2' H 2.147 . . 10 12 2 DC H2'' H 2.419 . . 11 12 2 DC H3' H 4.868 . . 12 12 2 DC H4' H 4.164 . . 13 12 2 DC H5 H 5.838 . . 14 12 2 DC H6 H 7.575 . . 15 12 2 DC H41 H 7.033 . . 16 12 2 DC H42 H 7.837 . . 17 12 2 DC P P 3.602 . . 18 13 3 DG H1' H 5.606 . . 19 13 3 DG H2' H 2.735 . . 20 13 3 DG H2'' H 2.772 . . 21 13 3 DG H3' H 5.004 . . 22 13 3 DG H4' H 4.365 . . 23 13 3 DG H5' H 4.07 . . 24 13 3 DG H5'' H 4.043 . . 25 13 3 DG H8 H 7.91 . . 26 13 3 DG P P 3.992 . . 27 14 4 DG H1' H 5.92 . . 28 14 4 DG H2' H 2.578 . . 29 14 4 DG H2'' H 2.726 . . 30 14 4 DG H3' H 5.013 . . 31 14 4 DG H4' H 4.424 . . 32 14 4 DG H5' H 4.167 . . 33 14 4 DG H5'' H 4.193 . . 34 14 4 DG H8 H 7.793 . . 35 14 4 DG P P 3.681 . . 36 15 5 DC H1' H 5.677 . . 37 15 5 DC H2' H 1.868 . . 38 15 5 DC H2'' H 2.326 . . 39 15 5 DC H3' H 4.852 . . 40 15 5 DC H4' H 4.121 . . 41 15 5 DC H5 H 5.289 . . 42 15 5 DC H6 H 7.231 . . 43 15 5 DC H41 H 6.341 . . 44 15 5 DC H42 H 8.342 . . 45 15 5 DC P P 3.55 . . 46 16 6 DG H1' H 5.634 . . 47 16 6 DG H2' H 2.706 . . 48 16 6 DG H2'' H 2.76 . . 49 16 6 DG H3' H 5.026 . . 50 16 6 DG H4' H 4.409 . . 51 16 6 DG P P 3.796 . . 52 17 7 DG H1' H 5.908 . . 53 17 7 DG H2' H 2.579 . . 54 17 7 DG H2'' H 2.721 . . 55 17 7 DG H3' H 4.97 . . 56 17 7 DG H4' H 4.433 . . 57 17 7 DG H5' H 4.069 . . 58 17 7 DG H5'' H 4.047 . . 59 17 7 DG H8 H 7.754 . . 60 17 7 DG P P 3.812 . . 61 18 8 DC H1' H 5.959 . . 62 18 8 DC H2' H 2.036 . . 63 18 8 DC H2'' H 2.427 . . 64 18 8 DC H3' H 4.837 . . 65 18 8 DC H4' H 4.195 . . 66 18 8 DC H5 H 5.331 . . 67 18 8 DC H6 H 7.367 . . 68 18 8 DC H42 H 8.269 . . 69 19 9 DC H1' H 5.672 . . 70 19 9 DC H2' H 1.99 . . 71 19 9 DC H2'' H 2.334 . . 72 19 9 DC H3' H 4.841 . . 73 19 9 DC H4' H 4.1 . . 74 19 9 DC H5 H 5.665 . . 75 19 9 DC H6 H 7.469 . . 76 19 9 DC H41 H 6.982 . . 77 19 9 DC H42 H 8.704 . . 78 20 10 DG H1' H 6.205 . . 79 20 10 DG H2' H 2.518 . . 80 20 10 DG H2'' H 2.387 . . 81 20 10 DG H3' H 4.71 . . 82 20 10 DG H4' H 4.201 . . 83 20 10 DG H5'' H 4.121 . . 84 20 10 DG H8 H 7.976 . . 85 20 10 DG P P 3.968 . . stop_ save_