data_30117 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structural impact of single ribonucleotides in DNA ; _BMRB_accession_number 30117 _BMRB_flat_file_name bmr30117.str _Entry_type original _Submission_date 2016-06-16 _Accession_date 2016-06-16 _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 Evich M. . . 2 Spring-Connell A. M. . 3 Storici F. . . 4 Germann M. W. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 128 "31P chemical shifts" 16 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-02-23 update BMRB 'update entry citation' 2016-08-22 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 30105 "DNA/RNA (5'-D(*AP*TP*GP*GP*A)-R(P*G)-D(P*CP*TP*C)-3'), DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')" 30111 "DNA (5'-D(*AP*TP*CP*CP*GP*GP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')" 30112 "DNA (5'-D(*TP*TP*AP*GP*GP*CP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3')" 30113 "DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')" 30114 "DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3')" 30115 "DNA/RNA (5'-D(*AP*TP*GP*GP*A)-R(P*G)-D(P*CP*TP*C)-3'), DNA (5'-D(*GP*AP*GP*CP*TP*CP*CP*AP*T)-3')" 30116 "DNA/RNA (5'-D(*AP*TP*CP*C)-R(P*G)-D(P*GP*TP*AP*G)-3'), DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')" stop_ _Original_release_date 2016-08-22 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural impact of single ribonucleotides in DNA. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27504600 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Evich M. . . 2 Spring-Connell A. M. . 3 Storici F. . . 4 Germann M. W. . stop_ _Journal_abbreviation Chembiochem _Journal_volume 17 _Journal_issue 20 _Journal_ISSN 1439-7633 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1968 _Page_last 1977 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-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/RNA hybrid" _Name_common entity_1 _Molecular_mass 2762.809 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence ; TTAGGCCTG ; loop_ _Residue_seq_code _Residue_label 1 DT 2 DT 3 DA 4 DG 5 G 6 DC 7 DC 8 DT 9 DG 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 entity_2 _Molecular_mass 2724.812 _Mol_thiol_state 'not present' _Details . _Residue_count 9 _Mol_residue_sequence ; CAGGCCTAA ; loop_ _Residue_seq_code _Residue_label 1 DC 2 DA 3 DG 4 DG 5 DC 6 DC 7 DT 8 DA 9 DA 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 . 32630 . . . . $entity_2 . 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' . . . . . $entity_2 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details ; 1 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3'), 100 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate, 100% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling D2O 100 % '100% deuterium' $entity_2 1 mM 'natural abundance' $entity_1 1 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details ; 1 mM DNA/RNA (5'-D(*TP*TP*AP*G)-R(P*G)-D(P*CP*CP*TP*G)-3'), 1 mM DNA (5'-D(*CP*AP*GP*GP*CP*CP*TP*AP*A)-3'), 10 % 100% deuterium D2O, 100 mM sodium chloride, 10 mM sodium phosphate, 90% H2O/10% D2O ; loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling D2O 10 % '100% deuterium' $entity_2 1 mM 'natural abundance' $entity_1 1 mM 'natural abundance' 'sodium chloride' 100 mM 'natural abundance' 'sodium phosphate' 10 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name AMBER _Version 9 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name CORMA _Version . loop_ _Vendor _Address _Electronic_address 'Thomas James' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_3 _Saveframe_category software _Name MARDIGRAS _Version . loop_ _Vendor _Address _Electronic_address 'Thomas James' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_4 _Saveframe_category software _Name SPARKY _Version 3.33 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_5 _Saveframe_category software _Name TOPSPIN _Version . 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 AvanceIII _Field_strength 850 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_250_ms_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY 250 ms' _Sample_label $sample_1 save_ save_2D_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_2 save_ save_2D_Low_Flip_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D Low Flip COSY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_constant_time_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D constant time NOESY' _Sample_label $sample_1 save_ save_1D_1H_1-1_jump_and_return_6 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H 1-1 jump and return' _Sample_label $sample_2 save_ save_1D_31P_7 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 31P' _Sample_label $sample_1 save_ save_1D_1H_8 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H' _Sample_label $sample_1 save_ save_2D_NOESY_150_ms_9 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY 150 ms' _Sample_label $sample_1 save_ save_2D_1H-31P_CORR_10 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-31P CORR' _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' 110 . mM pH 6.6 . pH pressure 1 . atm temperature 294 . 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' 110 . mM pH 7.0 . pH pressure 1 . atm temperature 294 . 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 'phosphoric acid' P 31 phosphorus ppm 0.000 external 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_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_4 stop_ loop_ _Experiment_label '2D NOESY 250 ms' '2D NOESY 150 ms' '2D 1H-31P CORR' 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 DT H1' H 6.021 0.004 . 2 1 1 DT H2' H 2.141 0.002 . 3 1 1 DT H2'' H 2.519 0.003 . 4 1 1 DT H3' H 4.726 0.002 . 5 1 1 DT H4' H 4.122 0.002 . 6 1 1 DT H6 H 7.555 0.001 . 7 1 1 DT H71 H 1.707 0.002 . 8 1 1 DT H72 H 1.707 0.002 . 9 1 1 DT H73 H 1.707 0.002 . 10 2 2 DT H1' H 5.672 0.002 . 11 2 2 DT H2' H 2.170 0.006 . 12 2 2 DT H2'' H 2.425 0.004 . 13 2 2 DT H3' H 4.878 0.003 . 14 2 2 DT H4' H 4.164 0.002 . 15 2 2 DT H6 H 7.544 0.002 . 16 2 2 DT H71 H 1.809 0.002 . 17 2 2 DT H72 H 1.809 0.002 . 18 2 2 DT H73 H 1.809 0.002 . 19 2 2 DT P P -0.79 . . 20 3 3 DA H1' H 6.067 0.002 . 21 3 3 DA H2 H 7.604 0.002 . 22 3 3 DA H2' H 2.765 0.002 . 23 3 3 DA H2'' H 2.907 0.002 . 24 3 3 DA H3' H 5.068 0.003 . 25 3 3 DA H4' H 4.429 0.002 . 26 3 3 DA H8 H 8.239 0.002 . 27 3 3 DA P P -0.54 . . 28 4 4 DG H1' H 5.684 0.004 . 29 4 4 DG H2' H 2.626 0.003 . 30 4 4 DG H2'' H 2.669 0.004 . 31 4 4 DG H3' H 4.945 0.001 . 32 4 4 DG H4' H 4.425 0.002 . 33 4 4 DG H8 H 7.640 0.001 . 34 4 4 DG P P -0.50 . . 35 5 5 G H1' H 5.662 0.002 . 36 5 5 G H2' H 4.524 0.011 . 37 5 5 G H3' H 4.543 0.001 . 38 5 5 G H4' H 4.504 0.003 . 39 5 5 G H8 H 7.484 0.002 . 40 5 5 G P P 0.02 . . 41 6 6 DC H1' H 5.849 0.004 . 42 6 6 DC H2' H 2.379 0.006 . 43 6 6 DC H2'' H 2.490 0.005 . 44 6 6 DC H3' H 4.643 0.004 . 45 6 6 DC H4' H 4.192 0.003 . 46 6 6 DC H5 H 5.206 0.002 . 47 6 6 DC H6 H 7.570 0.002 . 48 6 6 DC P P -0.44 . . 49 7 7 DC H1' H 5.915 0.002 . 50 7 7 DC H2' H 2.135 0.004 . 51 7 7 DC H2'' H 2.481 0.004 . 52 7 7 DC H3' H 4.748 0.003 . 53 7 7 DC H4' H 4.160 0.002 . 54 7 7 DC H5 H 5.580 0.003 . 55 7 7 DC H6 H 7.681 0.002 . 56 7 7 DC P P -0.87 . . 57 8 8 DT H1' H 5.925 0.002 . 58 8 8 DT H2' H 2.023 0.003 . 59 8 8 DT H2'' H 2.413 0.003 . 60 8 8 DT H3' H 4.876 0.002 . 61 8 8 DT H4' H 4.178 0.004 . 62 8 8 DT H6 H 7.463 0.003 . 63 8 8 DT H71 H 1.697 0.002 . 64 8 8 DT H72 H 1.697 0.002 . 65 8 8 DT H73 H 1.697 0.002 . 66 8 8 DT P P -1.02 . . 67 9 9 DG H1' H 6.183 0.002 . 68 9 9 DG H2' H 2.393 0.004 . 69 9 9 DG H2'' H 2.634 0.003 . 70 9 9 DG H3' H 4.703 0.003 . 71 9 9 DG H4' H 4.190 0.003 . 72 9 9 DG H8 H 7.953 0.001 . 73 9 9 DG P P -0.54 . . stop_ save_ save_assigned_chemical_shifts_1_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_4 stop_ loop_ _Experiment_label '2D NOESY 250 ms' '2D NOESY 150 ms' '2D 1H-31P CORR' 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 10 1 DC H1' H 5.649 0.003 . 2 10 1 DC H2' H 1.915 0.004 . 3 10 1 DC H2'' H 2.365 0.004 . 4 10 1 DC H3' H 4.700 0.002 . 5 10 1 DC H4' H 4.058 0.003 . 6 10 1 DC H5 H 5.957 0.003 . 7 10 1 DC H6 H 7.683 0.002 . 8 11 2 DA H1' H 6.034 0.004 . 9 11 2 DA H2 H 7.813 0.001 . 10 11 2 DA H2' H 2.785 0.002 . 11 11 2 DA H2'' H 2.934 0.002 . 12 11 2 DA H3' H 5.046 0.003 . 13 11 2 DA H4' H 4.393 0.004 . 14 11 2 DA H8 H 8.264 0.002 . 15 11 2 DA P P -0.53 . . 16 12 3 DG H1' H 5.679 0.003 . 17 12 3 DG H2' H 2.609 0.006 . 18 12 3 DG H2'' H 2.675 0.002 . 19 12 3 DG H3' H 4.995 0.002 . 20 12 3 DG H4' H 4.408 0.004 . 21 12 3 DG H8 H 7.667 0.002 . 22 12 3 DG P P -0.61 . . 23 13 4 DG H1' H 5.947 0.001 . 24 13 4 DG H2' H 2.564 0.002 . 25 13 4 DG H2'' H 2.706 0.003 . 26 13 4 DG H3' H 4.886 0.002 . 27 13 4 DG H4' H 4.417 0.003 . 28 13 4 DG H8 H 7.608 0.001 . 29 13 4 DG P P -0.36 . . 30 14 5 DC H1' H 5.938 0.003 . 31 14 5 DC H2' H 2.211 0.004 . 32 14 5 DC H2'' H 2.507 0.002 . 33 14 5 DC H3' H 4.767 0.003 . 34 14 5 DC H4' H 4.229 0.002 . 35 14 5 DC H5 H 5.174 0.003 . 36 14 5 DC H6 H 7.346 0.001 . 37 14 5 DC P P -0.67 . . 38 15 6 DC H1' H 5.867 0.004 . 39 15 6 DC H2' H 2.016 0.005 . 40 15 6 DC H2'' H 2.434 0.004 . 41 15 6 DC H3' H 4.757 0.002 . 42 15 6 DC H4' H 4.123 0.002 . 43 15 6 DC H5 H 5.486 0.002 . 44 15 6 DC H6 H 7.502 0.004 . 45 15 6 DC P P -0.69 . . 46 16 7 DT H1' H 5.609 0.003 . 47 16 7 DT H2' H 1.936 0.004 . 48 16 7 DT H2'' H 2.265 0.004 . 49 16 7 DT H3' H 4.830 0.005 . 50 16 7 DT H4' H 4.109 0.002 . 51 16 7 DT H6 H 7.355 0.002 . 52 16 7 DT H71 H 1.667 0.003 . 53 16 7 DT H72 H 1.667 0.003 . 54 16 7 DT H73 H 1.667 0.003 . 55 16 7 DT P P -0.94 . . 56 17 8 DA H1' H 5.969 0.002 . 57 17 8 DA H2 H 7.431 0.002 . 58 17 8 DA H2' H 2.674 0.003 . 59 17 8 DA H2'' H 2.772 0.003 . 60 17 8 DA H3' H 5.011 0.002 . 61 17 8 DA H4' H 4.348 0.001 . 62 17 8 DA H8 H 8.124 0.003 . 63 17 8 DA P P -0.62 . . 64 18 9 DA H1' H 6.191 0.002 . 65 18 9 DA H2 H 7.689 0.006 . 66 18 9 DA H2' H 2.581 0.004 . 67 18 9 DA H2'' H 2.369 0.003 . 68 18 9 DA H3' H 4.691 0.002 . 69 18 9 DA H4' H 4.205 0.003 . 70 18 9 DA H8 H 8.117 0.003 . 71 18 9 DA P P -0.60 . . stop_ save_