data_30054 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR solution structure of [Sp, Sp]-PT dsDNA ; _BMRB_accession_number 30054 _BMRB_flat_file_name bmr30054.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 Hu Zhongpei . . 3 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" 112 "31P chemical shifts" 18 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-11-14 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 30052 '[Rp, Rp]-PT dsDNA' 30053 'PT-free dsDNA from Streptomyces lividans' stop_ _Original_release_date 2016-11-14 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*(SSG)P*CP*CP*GP*CP*CP*GP*A)-3'), DNA (5'-D(*TP*CP*GP*GP*CP*GP*(SSG)P*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*(SSG)P*CP*CP*GP*CP*CP*GP*A)-3')" _Molecular_mass 3047.047 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 10 _Mol_residue_sequence ; CGXCCGCCGA ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 GS 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*(SSG)P*CP*CP*G)-3')" _Molecular_mass 3078.058 _Mol_thiol_state 'not present' _Details . _Residue_count 10 _Mol_residue_sequence ; TCGGCGXCCG ; 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 GS 8 18 DC 9 19 DC 10 20 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_GS _Saveframe_category polymer_residue _Mol_type 'DNA LINKING' _Name_common GUANOSINE-5'-THIO-MONOPHOSPHATE _BMRB_code GS _PDB_code GS _Standard_residue_derivative . _Molecular_mass 363.287 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons P P P . 0 . ? OP1 OP1 O . 0 . ? S2P S2P S . 0 . ? OP3 OP3 O . 0 . ? O5' O5' O . 0 . ? C5' C5' C . 0 . ? C4' C4' C . 0 . ? O4' O4' O . 0 . ? C3' C3' C . 0 . ? O3' O3' O . 0 . ? C2' C2' C . 0 . ? C1' C1' C . 0 . ? N9 N9 N . 0 . ? C8 C8 C . 0 . ? N7 N7 N . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? O6 O6 O . 0 . ? N1 N1 N . 0 . ? C2 C2 C . 0 . ? N2 N2 N . 0 . ? N3 N3 N . 0 . ? C4 C4 C . 0 . ? HSP2 HSP2 H . 0 . ? HOP3 HOP3 H . 0 . ? H5' H5' H . 0 . ? H5'' H5'' H . 0 . ? H4' H4' H . 0 . ? H3' H3' H . 0 . ? HO3' HO3' H . 0 . ? H2' H2' H . 0 . ? H2'' H2'' H . 0 . ? H1' H1' H . 0 . ? H8 H8 H . 0 . ? HN1 HN1 H . 0 . ? HN21 HN21 H . 0 . ? HN22 HN22 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB P OP1 ? ? SING P S2P ? ? SING P OP3 ? ? SING P O5' ? ? SING S2P HSP2 ? ? SING OP3 HOP3 ? ? SING O5' C5' ? ? SING C5' C4' ? ? SING C5' H5' ? ? SING C5' H5'' ? ? SING C4' O4' ? ? SING C4' C3' ? ? SING C4' H4' ? ? SING O4' C1' ? ? SING C3' O3' ? ? SING C3' C2' ? ? SING C3' H3' ? ? SING O3' HO3' ? ? SING C2' C1' ? ? SING C2' H2' ? ? SING C2' H2'' ? ? SING C1' N9 ? ? SING C1' H1' ? ? SING N9 C8 ? ? SING N9 C4 ? ? DOUB C8 N7 ? ? SING C8 H8 ? ? SING N7 C5 ? ? SING C5 C6 ? ? DOUB C5 C4 ? ? DOUB C6 O6 ? ? SING C6 N1 ? ? SING N1 C2 ? ? SING N1 HN1 ? ? SING C2 N2 ? ? DOUB C2 N3 ? ? SING N2 HN21 ? ? SING N2 HN22 ? ? SING N3 C4 ? ? stop_ 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 Sp dsDNA, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement '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_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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_1H-1H_DQCOSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H DQCOSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H 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 . mM pH 7.0 0.1 pH pressure 1.0 . atm temperature 298 . 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 . mM pH 7.0 . pH pressure 1.0 . atm temperature 298 . 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_1 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-31P HETCOR' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _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 5.766 . . 2 1 1 DC H2'' H 1.826 . . 3 1 1 DC H3' H 4.707 . . 4 1 1 DC H4' H 3.651 . . 5 1 1 DC H5 H 5.919 . . 6 1 1 DC H6 H 7.523 . . 7 2 2 DG H1' H 5.236 . . 8 2 2 DG H2'' H 2.648 . . 9 2 2 DG H3' H 4.962 . . 10 2 2 DG H4' H 4.273 . . 11 2 2 DG H5'' H 3.935 . . 12 2 2 DG H8 H 7.921 . . 13 2 2 DG P P 3.808 . . 14 3 3 GS H1' H 5.726 . . 15 3 3 GS H2' H 2.332 . . 16 3 3 GS H3' H 5.022 . . 17 3 3 GS P P 5.172 . . 18 4 4 DC H1' H 5.808 . . 19 4 4 DC H2'' H 1.969 . . 20 4 4 DC H3' H 4.799 . . 21 4 4 DC H4' H 4.189 . . 22 4 4 DC H5 H 6.764 . . 23 4 4 DC H6 H 7.548 . . 24 4 4 DC H41 H 8.554 . . 25 4 4 DC P P 3.467 . . 26 5 5 DC H1' H 5.69 . . 27 5 5 DC H2'' H 2.043 . . 28 5 5 DC H3' H 4.812 . . 29 5 5 DC H4' H 4.045 . . 30 5 5 DC H5 H 5.498 . . 31 5 5 DC H6 H 7.351 . . 32 5 5 DC P P 4.136 . . 33 6 6 DG H1' H 6.586 . . 34 6 6 DG H2'' H 2.467 . . 35 6 6 DG H3' H 4.867 . . 36 6 6 DG H4' H 4.204 . . 37 6 6 DG H5'' H 3.99 . . 38 6 6 DG H8 H 8.066 . . 39 6 6 DG P P 4.014 . . 40 7 7 DC H1' H 5.737 . . 41 7 7 DC H2'' H 1.989 . . 42 7 7 DC H3' H 4.806 . . 43 7 7 DC H4' H 4.148 . . 44 7 7 DC H5 H 5.769 . . 45 7 7 DC H6 H 7.454 . . 46 7 7 DC P P 3.49 . . 47 8 8 DC H1' H 5.465 . . 48 8 8 DC H2'' H 1.942 . . 49 8 8 DC H3' H 4.758 . . 50 8 8 DC H4' H 4.019 . . 51 8 8 DC H5 H 5.689 . . 52 8 8 DC H5'' H 4.002 . . 53 8 8 DC H6 H 7.429 . . 54 8 8 DC P P 4.013 . . 55 9 9 DG H1' H 5.663 . . 56 9 9 DG H2'' H 2.497 . . 57 9 9 DG H3' H 4.88 . . 58 9 9 DG H4' H 4.244 . . 59 9 9 DG H5'' H 3.902 . . 60 9 9 DG H8 H 7.891 . . 61 9 9 DG P P 3.875 . . 62 10 10 DA H1' H 6.324 . . 63 10 10 DA H2'' H 2.433 . . 64 10 10 DA H3' H 4.738 . . 65 10 10 DA H4' H 4.146 . . 66 10 10 DA H8 H 8.158 . . 67 10 10 DA P P 3.771 . . stop_ save_ save_assigned_chemical_shifts_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_1 stop_ loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-31P HETCOR' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_2 _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 6.07 . . 2 11 1 DT H2'' H 2.094 . . 3 11 1 DT H3' H 4.725 . . 4 11 1 DT H5'' H 3.671 . . 5 11 1 DT H6 H 7.493 . . 6 12 2 DC H1' H 5.562 . . 7 12 2 DC H2'' H 2.125 . . 8 12 2 DC H3' H 4.803 . . 9 12 2 DC H4' H 4.003 . . 10 12 2 DC H5 H 5.817 . . 11 12 2 DC H5'' H 3.676 . . 12 12 2 DC H6 H 7.546 . . 13 12 2 DC P P 3.614 . . 14 13 3 DG H1' H 5.603 . . 15 13 3 DG H2'' H 2.61 . . 16 13 3 DG H3' H 4.976 . . 17 13 3 DG H4' H 4.37 . . 18 13 3 DG H8 H 7.88 . . 19 13 3 DG P P 4.014 . . 20 14 4 DG H1' H 5.907 . . 21 14 4 DG H2'' H 2.555 . . 22 14 4 DG H3' H 4.913 . . 23 14 4 DG H4' H 4.381 . . 24 14 4 DG H8 H 7.773 . . 25 14 4 DG P P 3.817 . . 26 15 5 DC H1' H 5.747 . . 27 15 5 DC H2'' H 1.771 . . 28 15 5 DC H3' H 4.808 . . 29 15 5 DC H4' H 4.076 . . 30 15 5 DC H5 H 5.381 . . 31 15 5 DC H6 H 7.16 . . 32 15 5 DC P P 3.537 . . 33 16 6 DG H1' H 5.322 . . 34 16 6 DG H2'' H 2.616 . . 35 16 6 DG H3' H 5.059 . . 36 16 6 DG H4' H 4.267 . . 37 16 6 DG H8 H 7.836 . . 38 16 6 DG P P 3.607 . . 39 17 7 GS H1' H 6.12 . . 40 17 7 GS H2' H 2.485 . . 41 17 7 GS H3' H 4.961 . . 42 17 7 GS H8 H 7.943 . . 43 17 7 GS P P 5.239 . . 44 18 8 DC H1' H 5.972 . . 45 18 8 DC H2'' H 1.993 . . 46 18 8 DC H3' H 4.807 . . 47 18 8 DC H4' H 4.076 . . 48 18 8 DC H5 H 5.427 . . 49 18 8 DC H6 H 7.331 . . 50 18 8 DC P P 4.007 . . 51 19 9 DC H1' H 5.498 . . 52 19 9 DC H2'' H 1.883 . . 53 19 9 DC H3' H 4.796 . . 54 19 9 DC H4' H 4.269 . . 55 19 9 DC H5 H 5.649 . . 56 19 9 DC H6 H 7.37 . . 57 19 9 DC P P 3.601 . . 58 20 10 DG H1' H 5.952 . . 59 20 10 DG H2'' H 2.186 . . 60 20 10 DG H3' H 4.763 . . 61 20 10 DG H4' H 4.173 . . 62 20 10 DG H8 H 7.533 . . 63 20 10 DG P P 4.132 . . stop_ save_