data_34245 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Concerted dynamics of metallo-base pairs in an A/B-form helical transition (minor species) ; _BMRB_accession_number 34245 _BMRB_flat_file_name bmr34245.str _Entry_type original _Submission_date 2018-03-11 _Accession_date 2018-03-11 _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 Schmidt O. P. . 2 Jurt S. . . 3 Johannsen S. . . 4 Karimi A. . . 5 Sigel R. K.O. . 6 Luedtke N. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 150 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-11-05 update author 'update entry citation.' 2019-10-18 update author 'update entry citation, etc.' 2019-10-03 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 34244 'Concerted dynamics of metallo-base pairs in an A/B-form helical transition (major species)' 34398 'Concerted dynamics of metallo-base pairs in an A/B-form helical transition (apo species)' stop_ _Original_release_date 2018-05-24 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Concerted dynamics of metallo-base pairs in an A/B-form helical transition ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 31645548 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schmidt O. P. . 2 Jurt S. . . 3 Johannsen S. . . 4 Karimi A. . . 5 Sigel R. K.O. . 6 Luedtke N. W. . stop_ _Journal_abbreviation 'Nat. Commun.' _Journal_name_full 'Nature communications' _Journal_volume 10 _Journal_issue 1 _Journal_ISSN 2041-1723 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 4818 _Page_last 4818 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_minor" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'entity_1, 1' $entity_1 'entity_1, 2' $entity_1 'entity_2, 1' $entity_HG 'entity_2, 2' $entity_HG 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*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3')_minor" _Molecular_mass 4255.778 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence ; CGTCTCATGATACG ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DG 3 DT 4 DC 5 DT 6 DC 7 DA 8 DT 9 DG 10 DA 11 DT 12 DA 13 DC 14 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_HG _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common 'MERCURY (II) ION' _BMRB_code HG _PDB_code HG _Molecular_mass 200.590 _Mol_charge 2 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons HG HG HG . 2 . ? stop_ _Mol_thiol_state . _Sequence_homology_query_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 . 32630 . . . . 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 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION, 100% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.4 mM 'natural abundance' $entity_HG 1.2 mM '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 XPLOR-NIH _Version 2.46 loop_ _Vendor _Address _Electronic_address 'G. Marius Clore, Guillermo Bermejo, John Kuszewski, Charles D. Schwieters, and Nico Tjandra' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version 4.0.0.b.16 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _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' 50 . mM pH 7.35 . pD pressure 1 . 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 'Spectra measured at 298K' 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 _Reference_correction_type _Correction_value H2O H 1 protons ppm 4.70 internal direct . . . 1 temperature 0.07 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' 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, 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 5.814 0.002 . 2 1 1 DC H2' H 2.053 0.002 . 3 1 1 DC H2'' H 2.462 0.001 . 4 1 1 DC H5 H 5.933 0.001 . 5 1 1 DC H6 H 7.678 0.002 . 6 2 2 DG H1' H 6.094 0.002 . 7 2 2 DG H2' H 2.718 0.002 . 8 2 2 DG H2'' H 2.873 0.001 . 9 2 2 DG H8 H 8.017 0.002 . 10 3 3 DT H1' H 5.997 0.003 . 11 3 3 DT H2' H 2.179 0.002 . 12 3 3 DT H2'' H 2.554 0.003 . 13 3 3 DT H6 H 7.302 0.002 . 14 3 3 DT H71 H 1.533 0.002 . 15 3 3 DT H72 H 1.533 0.002 . 16 3 3 DT H73 H 1.533 0.002 . 17 4 4 DC H1' H 6.147 0.003 . 18 4 4 DC H2' H 2.145 0.003 . 19 4 4 DC H2'' H 2.610 0.002 . 20 4 4 DC H5 H 5.554 0.001 . 21 4 4 DC H6 H 7.530 0.002 . 22 5 5 DT H1' H 5.930 0.002 . 23 5 5 DT H2' H 2.125 0.002 . 24 5 5 DT H2'' H 2.473 0.002 . 25 5 5 DT H6 H 7.395 0.001 . 26 5 5 DT H71 H 1.709 0.002 . 27 5 5 DT H72 H 1.709 0.002 . 28 5 5 DT H73 H 1.709 0.002 . 29 6 6 DC H1' H 5.647 0.002 . 30 6 6 DC H2' H 2.160 0.001 . 31 6 6 DC H2'' H 2.468 0.001 . 32 6 6 DC H5 H 5.731 0.001 . 33 6 6 DC H6 H 7.592 0.001 . 34 7 7 DA H1' H 6.214 0.002 . 35 7 7 DA H2 H 7.557 0.000 . 36 7 7 DA H2' H 2.676 0.003 . 37 7 7 DA H2'' H 2.911 0.002 . 38 7 7 DA H8 H 8.329 0.002 . 39 8 8 DT H1' H 5.623 0.002 . 40 8 8 DT H2' H 1.913 0.001 . 41 8 8 DT H2'' H 2.303 0.003 . 42 8 8 DT H6 H 7.079 0.003 . 43 8 8 DT H71 H 1.442 0.002 . 44 8 8 DT H72 H 1.442 0.002 . 45 8 8 DT H73 H 1.442 0.002 . 46 9 9 DG H1' H 5.534 0.002 . 47 9 9 DG H2' H 2.593 0.003 . 48 9 9 DG H2'' H 2.704 0.002 . 49 9 9 DG H8 H 7.798 0.001 . 50 10 10 DA H1' H 6.156 0.001 . 51 10 10 DA H2 H 7.853 0.001 . 52 10 10 DA H2' H 2.557 0.003 . 53 10 10 DA H2'' H 2.822 0.002 . 54 10 10 DA H8 H 8.122 0.003 . 55 11 11 DT H1' H 5.417 0.001 . 56 11 11 DT H2' H 1.489 0.001 . 57 11 11 DT H2'' H 2.032 0.002 . 58 11 11 DT H6 H 6.926 0.003 . 59 11 11 DT H71 H 1.678 0.003 . 60 11 11 DT H72 H 1.678 0.003 . 61 11 11 DT H73 H 1.678 0.003 . 62 12 12 DA H1' H 6.118 0.002 . 63 12 12 DA H2 H 8.031 0.001 . 64 12 12 DA H2' H 2.741 0.002 . 65 12 12 DA H2'' H 2.780 0.002 . 66 12 12 DA H8 H 8.308 0.003 . 67 13 13 DC H1' H 5.693 0.003 . 68 13 13 DC H2' H 1.885 0.003 . 69 13 13 DC H2'' H 2.308 0.001 . 70 13 13 DC H5 H 5.400 0.002 . 71 13 13 DC H6 H 7.328 0.002 . 72 14 14 DG H1' H 6.167 0.002 . 73 14 14 DG H2' H 2.607 0.001 . 74 14 14 DG H2'' H 2.374 0.001 . 75 14 14 DG H8 H 7.901 0.001 . stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H NOESY' '2D 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC aliphatic' '2D 1H-13C HSQC aromatic' 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, 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 15 1 DC H1' H 5.814 0.002 . 2 15 1 DC H2' H 2.053 0.002 . 3 15 1 DC H2'' H 2.462 0.001 . 4 15 1 DC H5 H 5.933 0.001 . 5 15 1 DC H6 H 7.678 0.002 . 6 16 2 DG H1' H 6.094 0.002 . 7 16 2 DG H2' H 2.718 0.002 . 8 16 2 DG H2'' H 2.873 0.001 . 9 16 2 DG H8 H 8.017 0.002 . 10 17 3 DT H1' H 5.997 0.003 . 11 17 3 DT H2' H 2.179 0.002 . 12 17 3 DT H2'' H 2.554 0.003 . 13 17 3 DT H6 H 7.302 0.002 . 14 17 3 DT H71 H 1.533 0.002 . 15 17 3 DT H72 H 1.533 0.002 . 16 17 3 DT H73 H 1.533 0.002 . 17 18 4 DC H1' H 6.147 0.003 . 18 18 4 DC H2' H 2.145 0.003 . 19 18 4 DC H2'' H 2.610 0.002 . 20 18 4 DC H5 H 5.554 0.001 . 21 18 4 DC H6 H 7.530 0.002 . 22 19 5 DT H1' H 5.930 0.002 . 23 19 5 DT H2' H 2.125 0.002 . 24 19 5 DT H2'' H 2.473 0.002 . 25 19 5 DT H6 H 7.395 0.001 . 26 19 5 DT H71 H 1.709 0.002 . 27 19 5 DT H72 H 1.709 0.002 . 28 19 5 DT H73 H 1.709 0.002 . 29 20 6 DC H1' H 5.647 0.002 . 30 20 6 DC H2' H 2.160 0.001 . 31 20 6 DC H2'' H 2.468 0.001 . 32 20 6 DC H5 H 5.731 0.001 . 33 20 6 DC H6 H 7.592 0.001 . 34 21 7 DA H1' H 6.214 0.002 . 35 21 7 DA H2 H 7.557 0.000 . 36 21 7 DA H2' H 2.676 0.003 . 37 21 7 DA H2'' H 2.911 0.002 . 38 21 7 DA H8 H 8.329 0.002 . 39 22 8 DT H1' H 5.623 0.002 . 40 22 8 DT H2' H 1.913 0.001 . 41 22 8 DT H2'' H 2.303 0.003 . 42 22 8 DT H6 H 7.079 0.003 . 43 22 8 DT H71 H 1.442 0.002 . 44 22 8 DT H72 H 1.442 0.002 . 45 22 8 DT H73 H 1.442 0.002 . 46 23 9 DG H1' H 5.534 0.002 . 47 23 9 DG H2' H 2.593 0.003 . 48 23 9 DG H2'' H 2.704 0.002 . 49 23 9 DG H8 H 7.798 0.001 . 50 24 10 DA H1' H 6.156 0.001 . 51 24 10 DA H2 H 7.853 0.001 . 52 24 10 DA H2' H 2.557 0.003 . 53 24 10 DA H2'' H 2.822 0.002 . 54 24 10 DA H8 H 8.122 0.003 . 55 25 11 DT H1' H 5.417 0.001 . 56 25 11 DT H2' H 1.489 0.001 . 57 25 11 DT H2'' H 2.032 0.002 . 58 25 11 DT H6 H 6.926 0.003 . 59 25 11 DT H71 H 1.678 0.003 . 60 25 11 DT H72 H 1.678 0.003 . 61 25 11 DT H73 H 1.678 0.003 . 62 26 12 DA H1' H 6.118 0.002 . 63 26 12 DA H2 H 8.031 0.001 . 64 26 12 DA H2' H 2.741 0.002 . 65 26 12 DA H2'' H 2.780 0.002 . 66 26 12 DA H8 H 8.308 0.003 . 67 27 13 DC H1' H 5.693 0.003 . 68 27 13 DC H2' H 1.885 0.003 . 69 27 13 DC H2'' H 2.308 0.001 . 70 27 13 DC H5 H 5.400 0.002 . 71 27 13 DC H6 H 7.328 0.002 . 72 28 14 DG H1' H 6.167 0.002 . 73 28 14 DG H2' H 2.607 0.001 . 74 28 14 DG H2'' H 2.374 0.001 . 75 28 14 DG H8 H 7.901 0.001 . stop_ save_