data_16834 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of fully methylated GATC site ; _BMRB_accession_number 16834 _BMRB_flat_file_name bmr16834.str _Entry_type original _Submission_date 2010-04-04 _Accession_date 2010-04-04 _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 Bang Jongchul . . 2 Bae Sung-Hun . . 3 Park Chin-Ju . . 4 Lee Joon-Hwa . . 5 Choi Byong-Seok . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 137 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-27 original author . stop_ _Original_release_date 2010-07-27 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structural and dynamics study of DNA dodecamer duplexes that contain un-, hemi-, or fully methylated GATC sites.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19108701 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Bang Jongchul . . 2 Bae Sung-Hun . . 3 Park Chin-Ju . . 4 Lee Joon-Hwa . . 5 Choi Byong-Seok . . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 130 _Journal_issue 52 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 17688 _Page_last 17696 _Year 2008 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 5'-D(*DGP*DCP*DGP*DAP*DGP*(6MT)P*DTP*DCP*DTP*DGP*DCP*DG)-3' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA GCGAGATCTGCG' $DNA_1 'DNA CGCAGATCTCGC' $DNA_2 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_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_1 _Molecular_mass 3717.473 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 12 _Mol_residue_sequence GCGAGATCTGCG loop_ _Residue_seq_code _Residue_label 1 DG 2 DC 3 DG 4 DA 5 DG 6 DA 7 DT 8 DC 9 DT 10 DG 11 DC 12 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_2 _Molecular_mass 3637.424 _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence CGCAGATCTCGC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 13 DC 2 14 DG 3 15 DC 4 16 DA 5 17 DG 6 18 DA 7 19 DT 8 20 DC 9 21 DT 10 22 DC 11 23 DG 12 24 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_1 'E. coli' 562 Bacteria . Escherichia coli $DNA_2 'E. coli' 562 Bacteria . Escherichia coli stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $DNA_1 'recombinant technology' . chemical synthesis . 'not applicable' 'not applicable' $DNA_2 'recombinant technology' . chemical synthesis . 'not applicable' 'not applicable' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_dynamics _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $DNA_1 . mM 0.5 1.0 'natural abundance' $DNA_2 . mM 0.5 1.0 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ save_structure _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $DNA_1 . mM 0.5 1.0 'natural abundance' $DNA_2 . mM 0.5 1.0 'natural abundance' D2O 100 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_Felix _Saveframe_category software _Name FELIX _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_NMRDraw _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_VNMRJ _Saveframe_category software _Name VNMRJ _Version . loop_ _Vendor _Address _Electronic_address Varian . . stop_ loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $structure save_ save_2D_1H-1H_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $structure save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $structure save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $structure save_ save_2D_1H-13C_HSQC_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $structure save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $dynamics save_ save_2D_1H-1H_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $dynamics save_ ####################### # Sample conditions # ####################### save_structure_14c _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . pH temperature 287 . K stop_ save_ save_structure_35c _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . pH temperature 308 . K stop_ save_ save_structure_30c _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . pH temperature 303 . K stop_ save_ save_structure_15c _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.8 . pH temperature 288 . 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 . . . 1.000000000 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' '2D 1H-1H COSY' '2D 1H-1H TOCSY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $structure stop_ _Sample_conditions_label $structure_14c _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA GCGAGATCTGCG' _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 5.96 0.0005 1 2 1 1 DG H2' H 2.532 0.0011 1 3 1 1 DG H2'' H 2.592 0.0026 2 4 1 1 DG H3' H 4.766 0.0015 1 5 1 1 DG H8 H 7.881 0.0017 1 6 2 2 DC H1' H 5.403 0.001 1 7 2 2 DC H2' H 2.071 0.001 1 8 2 2 DC H2'' H 2.313 0.0035 2 9 2 2 DC H3' H 4.796 0.004 1 10 2 2 DC H5 H 5.633 0.0013 1 11 2 2 DC H6 H 7.489 0.0021 1 12 3 3 DG H1' H 5.245 0.0056 1 13 3 3 DG H2' H 2.671 0.0012 1 14 3 3 DG H3' H 4.958 0.0014 1 15 3 3 DG H8 H 7.909 0.0007 1 16 4 4 DA H1' H 6.04 0.0017 1 17 4 4 DA H2' H 2.703 0.0029 1 18 4 4 DA H2'' H 2.882 0.0027 2 19 4 4 DA H3' H 5.053 0.003 1 20 4 4 DA H4' H 4.423 0.0017 1 21 4 4 DA H8 H 8.106 0.0015 1 22 5 5 DG H1' H 5.64 0.0025 1 23 5 5 DG H2' H 2.527 0.0007 1 24 5 5 DG H2'' H 2.66 0.001 2 25 5 5 DG H3' H 4.983 0.0017 1 26 5 5 DG H4' H 4.441 0.0016 1 27 5 5 DG H8 H 7.644 0.0021 1 28 6 6 DA H1' H 6.221 0.0026 1 29 6 6 DA H2' H 2.549 0.0031 1 30 6 6 DA H2'' H 2.945 0.0017 2 31 6 6 DA H3' H 4.963 0.0016 1 32 6 6 DA H8 H 7.978 0.0014 1 33 7 7 DT H1' H 5.947 0.0016 1 34 7 7 DT H2' H 2.108 0.0026 1 35 7 7 DT H2'' H 2.531 0.0027 2 36 7 7 DT H3' H 4.867 0.0015 1 37 7 7 DT H6 H 7.157 0.0008 1 38 7 7 DT H71 H 1.254 0.0012 1 39 7 7 DT H72 H 1.254 0.0012 1 40 7 7 DT H73 H 1.254 0.0012 1 41 8 8 DC H1' H 6.026 0.0035 1 42 8 8 DC H2' H 2.117 0.0028 1 43 8 8 DC H2'' H 2.532 0.0032 2 44 8 8 DC H3' H 4.783 0.0019 1 45 8 8 DC H5 H 5.5 0.0021 1 46 8 8 DC H6 H 7.56 0.0038 1 47 9 9 DT H1' H 5.745 0.0015 1 48 9 9 DT H2' H 2.08 0.0037 1 49 9 9 DT H2'' H 2.429 0.0022 2 50 9 9 DT H3' H 4.882 0.0026 1 51 9 9 DT H6 H 7.309 0.001 1 52 9 9 DT H71 H 1.609 0.0013 1 53 9 9 DT H72 H 1.609 0.0013 1 54 9 9 DT H73 H 1.609 0.0013 1 55 10 10 DG H1' H 5.827 0.0005 1 56 10 10 DG H2'' H 2.653 0.0026 2 57 10 10 DG H3' H 4.974 0.0013 1 58 10 10 DG H4' H 4.353 0.0012 1 59 10 10 DG H8 H 7.926 0.002 1 60 11 11 DC H1' H 5.88 0.0006 1 61 11 11 DC H2' H 1.988 0.0021 1 62 11 11 DC H2'' H 2.424 0.0011 2 63 11 11 DC H3' H 4.776 0.0009 1 64 11 11 DC H5 H 5.482 0.0005 1 65 11 11 DC H6 H 7.409 0.0021 1 66 12 12 DG H1' H 6.117 0.0005 1 67 12 12 DG H2' H 2.341 0.0017 1 68 12 12 DG H2'' H 2.669 0.0015 2 69 12 12 DG H3' H 4.663 0.0005 1 70 12 12 DG H8 H 7.909 0.0012 1 stop_ save_ save_assigned_chem_shift_list_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' stop_ loop_ _Sample_label $structure stop_ _Sample_conditions_label $structure_14c _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'DNA CGCAGATCTCGC' _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 13 1 DC H1' H 5.82 0.0017 1 2 13 1 DC H2' H 1.915 0.0012 1 3 13 1 DC H2'' H 2.414 0.0014 2 4 13 1 DC H3' H 4.683 0.001 1 5 13 1 DC H5 H 5.985 0.0028 1 6 13 1 DC H6 H 7.786 0.0018 1 7 14 2 DG H1' H 5.92 0.0006 1 8 14 2 DG H2' H 2.713 0.0017 1 9 14 2 DG H3' H 4.954 0.0021 1 10 14 2 DG H4' H 4.359 0.0009 1 11 14 2 DG H8 H 8.004 0.0011 1 12 15 3 DC H1' H 5.488 0.002 1 13 15 3 DC H2' H 1.916 0.002 1 14 15 3 DC H2'' H 2.294 0.0021 2 15 15 3 DC H5 H 5.486 0.0005 1 16 15 3 DC H6 H 7.389 0.0017 1 17 16 4 DA H1' H 5.999 0.0022 1 18 16 4 DA H2' H 2.726 0.0023 1 19 16 4 DA H2'' H 2.884 0.0029 2 20 16 4 DA H3' H 5.035 0.0015 1 21 16 4 DA H4' H 4.384 0.0023 1 22 16 4 DA H8 H 8.156 0.0026 1 23 17 5 DG H1' H 5.619 0.0015 1 24 17 5 DG H2' H 2.536 0.0017 1 25 17 5 DG H2'' H 2.66 0.0015 2 26 17 5 DG H3' H 4.98 0.0019 1 27 17 5 DG H4' H 4.39 0.0007 1 28 17 5 DG H8 H 7.684 0.0013 1 29 18 6 DA H1' H 6.218 0.0028 1 30 18 6 DA H2 H 7.647 0.0012 1 31 18 6 DA H2' H 2.539 0 1 32 18 6 DA H2'' H 2.941 0.0019 2 33 18 6 DA H3' H 4.96 0.0023 1 34 18 6 DA H8 H 7.981 0.0015 1 35 19 7 DT H1' H 5.946 0.001 1 36 19 7 DT H2' H 2.105 0.0024 1 37 19 7 DT H3' H 4.868 0.002 1 38 19 7 DT H6 H 7.158 0.0006 1 39 19 7 DT H71 H 1.269 0.0008 1 40 19 7 DT H72 H 1.269 0.0008 1 41 19 7 DT H73 H 1.269 0.0008 1 42 20 8 DC H1' H 6.03 0.0025 1 43 20 8 DC H2'' H 2.542 0.0034 2 44 20 8 DC H5 H 5.503 0.0012 1 45 20 8 DC H6 H 7.563 0.0009 1 46 21 9 DT H2'' H 4.874 0.0031 2 47 21 9 DT H3 H 2.123 0.0012 2 48 21 9 DT H3' H 4.874 0.0011 2 49 21 9 DT H6 H 7.421 0.001 2 50 21 9 DT H71 H 1.269 0.0029 2 51 21 9 DT H72 H 1.269 0.0029 2 52 21 9 DT H73 H 1.269 0.0029 2 53 22 10 DC H1' H 5.437 0.003 1 54 22 10 DC H2' H 2.144 0.0036 1 55 22 10 DC H2'' H 2.395 0.0032 2 56 22 10 DC H5 H 5.707 0.0003 1 57 22 10 DC H6 H 7.566 0.002 1 58 23 11 DG H1' H 6.098 0.001 1 59 23 11 DG H2' H 2.655 0.0022 1 60 23 11 DG H2'' H 2.79 0.0016 2 61 23 11 DG H3' H 5.008 0.0008 1 62 23 11 DG H8 H 7.971 0.0022 1 63 24 12 DC H1' H 6.223 0.0004 1 64 24 12 DC H2' H 2.275 0.0033 1 65 24 12 DC H2'' H 2.345 0.0015 2 66 24 12 DC H5 H 5.777 0.0013 1 67 24 12 DC H6 H 7.787 0.001 1 stop_ save_