data_4733 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; HMG-D complexed to a bulge DNA: an NMR study ; _BMRB_accession_number 4733 _BMRB_flat_file_name bmr4733.str _Entry_type new _Submission_date 2000-05-03 _Accession_date 2000-05-03 _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 Cerdan Rachel . . 2 Payet Dominique . . 3 Yang Ji-Chun . . 4 Travers Andrew A. . 5 Neuhaus David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 203 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-07-15 update BMRB 'update DNA residue label to two-letter code' 2000-05-11 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 4732 'free HMG-D protein' 4734 'HMG-D protein - bulge DNA complex' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'HMG-D complexed to a bulge DNA: an NMR study' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Cerdan Rachel . . 2 Payet Dominique . . 3 Yang Ji-Chun . . 4 Travers Andrew A . 5 Neuhaus David . . stop_ _Journal_abbreviation 'Protein Sci.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year 2000 _Details . loop_ _Keyword 'HMG-D protein' 'bulge DNA' stop_ save_ ################################## # Molecular system description # ################################## save_bulge_DNA_12/14mer _Saveframe_category molecular_system _Mol_system_name 'bulge DNA 12/14mer' _Abbreviation_common 12/14mer _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'bulge DNA free 12/14mer strand 1' $14monomer 'bulge DNA free 12/14mer strand 2' $12monomer stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' loop_ _Biological_function 'DNA binding protein' 'chromatin-associated protein' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_14monomer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'bulge DNA 12/14mer' _Abbreviation_common 12/14mer _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence CGATATTAAGAGCC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DC 2 2 DG 3 3 DA 4 4 DT 5 5 DA 6 6 DT 7 7 DT 8 8 DA 9 9 DA 10 10 DG 11 11 DA 12 12 DG 13 13 DC 14 14 DC stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_12monomer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'bulge DNA 12/14mer' _Abbreviation_common 12/14mer _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 12 _Mol_residue_sequence GGCTCAATATCG loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 15 DG 2 16 DG 3 17 DC 4 18 DT 5 19 DC 6 20 DA 7 21 DA 8 22 DT 9 23 DA 10 24 DT 11 25 DC 12 26 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 $14monomer . . . . . . $12monomer . . . . . . 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 $14monomer 'chemical synthesis' . . . . . $12monomer 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $14monomer 1 mM . $12monomer 1 mM . stop_ save_ ############################ # Computer software used # ############################ save_Xwin-NMR _Saveframe_category software _Name Xwin-NMR _Version . _Details . save_ save_Felix _Saveframe_category software _Name Felix _Version . _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ save_NMR_spectrometer2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label . save_ save_3D_HNCA_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _Sample_label . save_ save_3D_CBCA(CO)NH_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label . save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCA' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.0 0.1 n/a temperature 303 1 K 'ionic strength' 0.005 . M stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 TSP H 1 'methyl protons' ppm 0.00 internal direct cylindrical internal parallel_to_Bo 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'bulge DNA free 12/14mer strand 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 DC H5 H 5.91 0.01 1 2 . 1 DC H6 H 7.61 0.01 1 3 . 1 DC H1' H 5.74 0.01 1 4 . 1 DC H2' H 1.91 0.01 1 5 . 1 DC H2'' H 2.40 0.01 1 6 . 1 DC H3' H 4.71 0.01 1 7 . 1 DC H4' H 4.07 0.01 1 8 . 2 DG H1 H 12.84 0.01 1 9 . 2 DG H8 H 7.95 0.01 1 10 . 2 DG H1' H 5.55 0.01 1 11 . 2 DG H2' H 2.75 0.01 1 12 . 2 DG H2'' H 2.83 0.01 1 13 . 2 DG H3' H 5.02 0.01 1 14 . 2 DG H4' H 4.34 0.01 1 15 . 3 DA H2 H 7.83 0.01 1 16 . 3 DA H8 H 8.26 0.01 1 17 . 3 DA H1' H 6.30 0.01 1 18 . 3 DA H2' H 2.71 0.01 1 19 . 3 DA H2'' H 2.99 0.01 1 20 . 3 DA H3' H 5.06 0.01 1 21 . 3 DA H4' H 4.51 0.01 1 22 . 4 DT H3 H 13.19 0.01 1 23 . 4 DT H6 H 7.15 0.01 1 24 . 4 DT H71 H 1.48 0.01 2 25 . 4 DT H72 H 1.48 0.01 2 26 . 4 DT H73 H 1.48 0.01 2 27 . 4 DT H1' H 5.70 0.01 1 28 . 4 DT H2' H 2.10 0.01 1 29 . 4 DT H2'' H 2.49 0.01 1 30 . 4 DT H3' H 4.91 0.01 1 31 . 4 DT H4' H 4.21 0.01 1 32 . 5 DA H2 H 7.29 0.01 1 33 . 5 DA H8 H 8.27 0.01 1 34 . 5 DA H1' H 6.25 0.01 1 35 . 5 DA H2' H 2.66 0.01 1 36 . 5 DA H2'' H 2.90 0.01 1 37 . 5 DA H3' H 5.02 0.01 1 38 . 5 DA H4' H 4.43 0.01 1 39 . 6 DT H3 H 13.72 0.01 1 40 . 6 DT H6 H 7.20 0.01 1 41 . 6 DT H71 H 1.46 0.01 2 42 . 6 DT H72 H 1.46 0.01 2 43 . 6 DT H73 H 1.46 0.01 2 44 . 6 DT H1' H 5.93 0.01 1 45 . 6 DT H2' H 1.91 0.01 1 46 . 6 DT H2'' H 2.40 0.01 1 47 . 6 DT H3' H 4.84 0.01 1 48 . 6 DT H4' H 4.13 0.01 1 49 . 7 DT H6 H 7.18 0.01 1 50 . 7 DT H71 H 1.67 0.01 2 51 . 7 DT H72 H 1.67 0.01 2 52 . 7 DT H73 H 1.67 0.01 2 53 . 7 DT H1' H 5.78 0.01 1 54 . 7 DT H2' H 1.69 0.01 1 55 . 7 DT H2'' H 2.08 0.01 1 56 . 7 DT H3' H 4.79 0.01 1 57 . 7 DT H4' H 3.98 0.01 1 58 . 8 DA H8 H 7.90 0.01 1 59 . 8 DA H1' H 5.62 0.01 1 60 . 8 DA H2' H 2.10 0.01 1 61 . 8 DA H2'' H 2.25 0.01 1 62 . 8 DA H3' H 4.87 0.01 1 63 . 8 DA H4' H 4.04 0.01 1 64 . 9 DA H8 H 7.92 0.01 1 65 . 9 DA H1' H 5.19 0.01 1 66 . 9 DA H2' H 2.40 0.01 1 67 . 9 DA H2'' H 2.40 0.01 1 68 . 9 DA H3' H 4.92 0.01 1 69 . 9 DA H4' H 4.18 0.01 1 70 . 10 DG H1 H 12.27 0.01 1 71 . 10 DG H8 H 7.81 0.01 1 72 . 10 DG H1' H 5.31 0.01 1 73 . 10 DG H2' H 2.68 0.01 1 74 . 10 DG H2'' H 2.68 0.01 1 75 . 10 DG H3' H 4.96 0.01 1 76 . 10 DG H4' H 4.29 0.01 1 77 . 11 DA H2 H 7.75 0.01 1 78 . 11 DA H8 H 8.08 0.01 1 79 . 11 DA H1' H 6.03 0.01 1 80 . 11 DA H2' H 2.71 0.01 1 81 . 11 DA H2'' H 2.88 0.01 1 82 . 11 DA H3' H 5.05 0.01 1 83 . 11 DA H4' H 4.43 0.01 1 84 . 12 DG H1 H 12.86 0.01 1 85 . 12 DG H8 H 7.64 0.01 1 86 . 12 DG H1' H 5.80 0.01 1 87 . 12 DG H2' H 2.53 0.01 1 88 . 12 DG H2'' H 2.66 0.01 1 89 . 12 DG H3' H 4.96 0.01 1 90 . 12 DG H4' H 4.39 0.01 1 91 . 13 DC H41 H 6.48 0.01 1 92 . 13 DC H42 H 8.22 0.01 1 93 . 13 DC H5 H 5.33 0.01 1 94 . 13 DC H6 H 7.39 0.01 1 95 . 13 DC H1' H 6.01 0.01 1 96 . 13 DC H2' H 2.15 0.01 1 97 . 13 DC H2'' H 2.47 0.01 1 98 . 13 DC H3' H 4.79 0.01 1 99 . 13 DC H4' H 4.15 0.01 1 100 . 14 DC H5 H 5.79 0.01 1 101 . 14 DC H6 H 7.68 0.01 1 102 . 14 DC H1' H 6.26 0.01 1 103 . 14 DC H2' H 2.27 0.01 1 104 . 14 DC H2'' H 2.27 0.01 1 105 . 14 DC H3' H 4.56 0.01 1 106 . 14 DC H4' H 4.06 0.01 1 stop_ save_ save_chemical_shifts_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'bulge DNA free 12/14mer strand 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 . 1 DG H8 H 7.85 0.01 1 2 . 1 DG H1' H 5.71 0.01 1 3 . 1 DG H2' H 2.53 0.01 1 4 . 1 DG H2'' H 2.71 0.01 1 5 . 1 DG H3' H 4.83 0.01 1 6 . 1 DG H4' H 4.19 0.01 1 7 . 2 DG H1 H 13.00 0.01 1 8 . 2 DG H8 H 7.84 0.01 1 9 . 2 DG H1' H 5.95 0.01 1 10 . 2 DG H2' H 2.73 0.01 1 11 . 2 DG H2'' H 2.73 0.01 1 12 . 2 DG H3' H 5.00 0.01 1 13 . 2 DG H4' H 4.43 0.01 1 14 . 3 DC H41 H 6.41 0.01 1 15 . 3 DC H42 H 8.09 0.01 1 16 . 3 DC H5 H 5.30 0.01 1 17 . 3 DC H6 H 7.42 0.01 1 18 . 3 DC H1' H 6.00 0.01 1 19 . 3 DC H2' H 2.08 0.01 1 20 . 3 DC H2'' H 2.51 0.01 1 21 . 3 DC H3' H 4.95 0.01 1 22 . 3 DC H4' H 4.26 0.01 1 23 . 4 DT H3 H 13.80 0.01 1 24 . 4 DT H6 H 7.39 0.01 1 25 . 4 DT H71 H 1.54 0.01 2 26 . 4 DT H72 H 1.54 0.01 2 27 . 4 DT H73 H 1.54 0.01 2 28 . 4 DT H1' H 6.05 0.01 1 29 . 4 DT H2' H 2.10 0.01 1 30 . 4 DT H2'' H 2.49 0.01 1 31 . 4 DT H3' H 4.87 0.01 1 32 . 4 DT H4' H 4.19 0.01 1 33 . 5 DC H41 H 6.80 0.01 1 34 . 5 DC H42 H 8.00 0.01 1 35 . 5 DC H5 H 5.63 0.01 1 36 . 5 DC H6 H 7.50 0.01 1 37 . 5 DC H1' H 6.18 0.01 1 38 . 5 DC H2' H 2.04 0.01 1 39 . 5 DC H2'' H 2.04 0.01 1 40 . 5 DC H3' H 4.95 0.01 1 41 . 5 DC H4' H 4.29 0.01 1 42 . 6 DA H2 H 7.26 0.01 1 43 . 6 DA H8 H 8.45 0.01 1 44 . 6 DA H1' H 6.05 0.01 1 45 . 6 DA H2' H 2.88 0.01 1 46 . 6 DA H2'' H 2.99 0.01 1 47 . 6 DA H3' H 5.07 0.01 1 48 . 6 DA H4' H 4.46 0.01 1 49 . 7 DA H2 H 7.75 0.01 1 50 . 7 DA H8 H 8.21 0.01 1 51 . 7 DA H1' H 6.16 0.01 1 52 . 7 DA H2' H 2.64 0.01 1 53 . 7 DA H2'' H 2.90 0.01 1 54 . 7 DA H3' H 5.01 0.01 1 55 . 7 DA H4' H 4.43 0.01 1 56 . 8 DT H3 H 13.13 0.01 1 57 . 8 DT H6 H 7.15 0.01 1 58 . 8 DT H71 H 1.39 0.01 2 59 . 8 DT H72 H 1.39 0.01 2 60 . 8 DT H73 H 1.39 0.01 2 61 . 8 DT H1' H 5.66 0.01 1 62 . 8 DT H2' H 2.12 0.01 1 63 . 8 DT H2'' H 2.49 0.01 1 64 . 8 DT H3' H 4.86 0.01 1 65 . 8 DT H4' H 4.19 0.01 1 66 . 9 DA H2 H 7.30 0.01 1 67 . 9 DA H8 H 8.25 0.01 1 68 . 9 DA H1' H 6.25 0.01 1 69 . 9 DA H2' H 2.64 0.01 1 70 . 9 DA H2'' H 2.92 0.01 1 71 . 9 DA H3' H 5.00 0.01 1 72 . 9 DA H4' H 4.41 0.01 1 73 . 10 DT H3 H 13.55 0.01 1 74 . 10 DT H6 H 7.20 0.01 1 75 . 10 DT H71 H 1.35 0.01 2 76 . 10 DT H72 H 1.35 0.01 2 77 . 10 DT H73 H 1.35 0.01 2 78 . 10 DT H1' H 5.94 0.01 1 79 . 10 DT H2' H 2.02 0.01 1 80 . 10 DT H2'' H 2.43 0.01 1 81 . 10 DT H3' H 4.86 0.01 1 82 . 10 DT H4' H 4.19 0.01 1 83 . 11 DC H41 H 6.93 0.01 1 84 . 11 DC H42 H 8.52 0.01 1 85 . 11 DC H5 H 5.66 0.01 1 86 . 11 DC H6 H 7.47 0.01 1 87 . 11 DC H1' H 5.73 0.01 1 88 . 11 DC H2' H 2.02 0.01 1 89 . 11 DC H2'' H 2.38 0.01 1 90 . 11 DC H3' H 4.84 0.01 1 91 . 11 DC H4' H 4.13 0.01 1 92 . 12 DG H8 H 7.94 0.01 1 93 . 12 DG H1' H 6.16 0.01 1 94 . 12 DG H2' H 2.62 0.01 1 95 . 12 DG H2'' H 2.38 0.01 1 96 . 12 DG H3' H 4.69 0.01 1 97 . 12 DG H4' H 4.19 0.01 1 stop_ save_