data_25307 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; solution structure of SATB1 homeodomain ; _BMRB_accession_number 25307 _BMRB_flat_file_name bmr25307.str _Entry_type original _Submission_date 2014-10-31 _Accession_date 2014-10-31 _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 Yamasaki Kazuhiko . . 2 Yamasaki Tomoko . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 "15N chemical shifts" 73 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-03-29 update BMRB 'update entry citation' 2015-11-02 original author 'original release' stop_ _Original_release_date 2015-11-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; The combination of sequence-specific and nonspecific DNA-binding modes of transcription factor SATB1 ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 27462121 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Yamasaki Kazuhiko . . 2 Yamasaki Tomoko . . stop_ _Journal_abbreviation 'Biochem. J.' _Journal_name_full 'The Biochemical journal' _Journal_volume 473 _Journal_issue 19 _Journal_ISSN 1470-8728 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 3321 _Page_last 3339 _Year 2016 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'SATB1 homeodomain' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SATB1 homeodomain' $SATB1 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_SATB1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common SATB1 _Molecular_mass 7903.208 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 71 _Mol_residue_sequence ; GSHMNRQKTRPRTKISVEAL GILQSFIQDVGLYPDEEAIQ TLSAQLDLPKYTIIKFFQNQ RYYLKHHGKLK ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 637 GLY 2 638 SER 3 639 HIS 4 640 MET 5 641 ASN 6 642 ARG 7 643 GLN 8 644 LYS 9 645 THR 10 646 ARG 11 647 PRO 12 648 ARG 13 649 THR 14 650 LYS 15 651 ILE 16 652 SER 17 653 VAL 18 654 GLU 19 655 ALA 20 656 LEU 21 657 GLY 22 658 ILE 23 659 LEU 24 660 GLN 25 661 SER 26 662 PHE 27 663 ILE 28 664 GLN 29 665 ASP 30 666 VAL 31 667 GLY 32 668 LEU 33 669 TYR 34 670 PRO 35 671 ASP 36 672 GLU 37 673 GLU 38 674 ALA 39 675 ILE 40 676 GLN 41 677 THR 42 678 LEU 43 679 SER 44 680 ALA 45 681 GLN 46 682 LEU 47 683 ASP 48 684 LEU 49 685 PRO 50 686 LYS 51 687 TYR 52 688 THR 53 689 ILE 54 690 ILE 55 691 LYS 56 692 PHE 57 693 PHE 58 694 GLN 59 695 ASN 60 696 GLN 61 697 ARG 62 698 TYR 63 699 TYR 64 700 LEU 65 701 LYS 66 702 HIS 67 703 HIS 68 704 GLY 69 705 LYS 70 706 LEU 71 707 LYS 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 $SATB1 human 9606 Eukaryota Metazoa Homo sapiens 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 $SATB1 'recombinant technology' . Escherichia coli BL21(DE3) pET15b 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 $SATB1 0.3 mM [U-15N] 'sodium phosphate' 50 mM 'natural abundance' 'sodium chloride' 50 mM 'natural abundance' DSS 0.5 mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $SATB1 . mM 0.7 1.2 [U-15N] 'sodium phosphate' 50 mM . . 'natural abundance' 'sodium chloride' 200 mM . . 'natural abundance' DSS 0.5 mM . . 'natural abundance' H2O 90 % . . 'natural abundance' D2O 5 % . . 'natural abundance' stop_ save_ save_sample_3 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $SATB1 . mM 0.7 1.2 [U-15N] 'sodium phosphate' 50 mM . . 'natural abundance' 'sodium chloride' 200 mM . . 'natural abundance' DSS 0.5 mM . . 'natural abundance' H2O 95 % . . 'natural abundance' D2O 5 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' 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_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ save_spectrometer_3 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_1 save_ save_2D_1H-15N_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample_2 save_ save_3D_1H-15N_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_2 save_ save_3D_1H-15N_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_3 save_ save_2D_DQF-COSY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_3 save_ save_2D_1H-1H_TOCSY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_3 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' 0.1 . M pH 5.5 . pH pressure 1 . 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' 0.25 . M pH 5.5 . pH pressure 1 . atm temperature 298 . 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 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'SATB1 homeodomain' _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 1 641 5 ASN H H 8.61 0.01 1 2 641 5 ASN HD21 H 6.98 0.01 2 3 641 5 ASN HD22 H 7.66 0.01 2 4 641 5 ASN N N 120.60 0.10 1 5 641 5 ASN ND2 N 113.10 0.10 1 6 642 6 ARG H H 8.39 0.01 1 7 642 6 ARG N N 121.90 0.10 1 8 643 7 GLN H H 8.41 0.01 1 9 643 7 GLN HE21 H 6.89 0.01 2 10 643 7 GLN HE22 H 7.55 0.01 2 11 643 7 GLN N N 121.30 0.10 1 12 643 7 GLN NE2 N 112.70 0.10 1 13 644 8 LYS H H 8.40 0.01 1 14 644 8 LYS N N 122.90 0.10 1 15 645 9 THR H H 8.16 0.01 1 16 645 9 THR N N 115.80 0.10 1 17 646 10 ARG H H 8.41 0.01 1 18 646 10 ARG N N 124.90 0.10 1 19 648 12 ARG H H 8.60 0.01 1 20 648 12 ARG N N 122.20 0.10 1 21 649 13 THR H H 8.25 0.01 1 22 649 13 THR N N 114.70 0.10 1 23 650 14 LYS H H 8.12 0.01 1 24 650 14 LYS N N 124.30 0.10 1 25 651 15 ILE H H 8.30 0.01 1 26 651 15 ILE N N 124.10 0.10 1 27 652 16 SER H H 8.73 0.01 1 28 652 16 SER N N 124.80 0.10 1 29 653 17 VAL H H 8.64 0.01 1 30 653 17 VAL N N 120.10 0.10 1 31 654 18 GLU H H 8.71 0.01 1 32 654 18 GLU N N 121.30 0.10 1 33 655 19 ALA H H 7.98 0.01 1 34 655 19 ALA N N 123.70 0.10 1 35 656 20 LEU H H 8.56 0.01 1 36 656 20 LEU N N 118.90 0.10 1 37 657 21 GLY H H 7.81 0.01 1 38 657 21 GLY N N 105.50 0.10 1 39 658 22 ILE H H 7.43 0.01 1 40 658 22 ILE N N 124.20 0.10 1 41 659 23 LEU H H 8.37 0.01 1 42 659 23 LEU N N 122.60 0.10 1 43 660 24 GLN H H 8.85 0.01 1 44 660 24 GLN HE21 H 6.73 0.01 2 45 660 24 GLN HE22 H 7.31 0.01 2 46 660 24 GLN N N 117.70 0.10 1 47 660 24 GLN NE2 N 110.10 0.10 1 48 661 25 SER H H 8.07 0.01 1 49 661 25 SER N N 116.80 0.10 1 50 662 26 PHE H H 8.14 0.01 1 51 662 26 PHE N N 123.80 0.10 1 52 663 27 ILE H H 8.41 0.01 1 53 663 27 ILE N N 120.80 0.10 1 54 664 28 GLN H H 7.75 0.01 1 55 664 28 GLN HE21 H 6.85 0.01 2 56 664 28 GLN HE22 H 7.60 0.01 2 57 664 28 GLN N N 117.50 0.10 1 58 664 28 GLN NE2 N 112.20 0.10 1 59 665 29 ASP H H 8.15 0.01 1 60 665 29 ASP N N 117.60 0.10 1 61 666 30 VAL H H 8.48 0.01 1 62 666 30 VAL N N 120.30 0.10 1 63 667 31 GLY H H 7.88 0.01 1 64 667 31 GLY N N 109.70 0.10 1 65 668 32 LEU H H 8.05 0.01 1 66 668 32 LEU N N 114.10 0.10 1 67 669 33 TYR H H 8.45 0.01 1 68 669 33 TYR N N 117.50 0.10 1 69 671 35 ASP H H 8.32 0.01 1 70 671 35 ASP N N 121.40 0.10 1 71 672 36 GLU H H 8.46 0.01 1 72 672 36 GLU N N 118.10 0.10 1 73 673 37 GLU H H 8.23 0.01 1 74 673 37 GLU N N 119.90 0.10 1 75 674 38 ALA H H 8.35 0.01 1 76 674 38 ALA N N 124.70 0.10 1 77 675 39 ILE H H 8.22 0.01 1 78 675 39 ILE N N 118.10 0.10 1 79 676 40 GLN H H 8.17 0.01 1 80 676 40 GLN HE21 H 6.91 0.01 2 81 676 40 GLN HE22 H 7.62 0.01 2 82 676 40 GLN N N 120.10 0.10 1 83 676 40 GLN NE2 N 112.20 0.10 1 84 677 41 THR H H 8.53 0.01 1 85 677 41 THR N N 118.60 0.10 1 86 678 42 LEU H H 8.48 0.01 1 87 678 42 LEU N N 122.80 0.10 1 88 679 43 SER H H 8.32 0.01 1 89 679 43 SER N N 113.50 0.10 1 90 680 44 ALA H H 7.86 0.01 1 91 680 44 ALA N N 121.50 0.10 1 92 681 45 GLN H H 8.45 0.01 1 93 681 45 GLN HE21 H 6.64 0.01 2 94 681 45 GLN HE22 H 7.31 0.01 2 95 681 45 GLN N N 118.10 0.10 1 96 681 45 GLN NE2 N 108.90 0.10 1 97 682 46 LEU H H 8.15 0.01 1 98 682 46 LEU N N 114.80 0.10 1 99 683 47 ASP H H 7.83 0.01 1 100 683 47 ASP N N 119.60 0.10 1 101 684 48 LEU H H 7.66 0.01 1 102 684 48 LEU N N 117.10 0.10 1 103 686 50 LYS H H 8.96 0.01 1 104 686 50 LYS N N 123.60 0.10 1 105 687 51 TYR H H 8.15 0.01 1 106 687 51 TYR N N 114.20 0.10 1 107 688 52 THR H H 6.97 0.01 1 108 688 52 THR N N 118.50 0.10 1 109 689 53 ILE H H 7.28 0.01 1 110 689 53 ILE N N 122.10 0.10 1 111 690 54 ILE H H 8.63 0.01 1 112 690 54 ILE N N 120.40 0.10 1 113 691 55 LYS H H 8.01 0.01 1 114 691 55 LYS N N 119.60 0.10 1 115 692 56 PHE H H 7.82 0.01 1 116 692 56 PHE N N 120.30 0.10 1 117 693 57 PHE H H 8.11 0.01 1 118 693 57 PHE N N 118.20 0.10 1 119 694 58 GLN H H 8.55 0.01 1 120 694 58 GLN HE21 H 6.85 0.01 2 121 694 58 GLN HE22 H 7.48 0.01 2 122 694 58 GLN N N 119.30 0.10 1 123 694 58 GLN NE2 N 111.30 0.10 1 124 695 59 ASN H H 8.56 0.01 1 125 695 59 ASN HD21 H 6.89 0.01 2 126 695 59 ASN HD22 H 7.63 0.01 2 127 695 59 ASN N N 118.90 0.10 1 128 695 59 ASN ND2 N 112.00 0.10 1 129 696 60 GLN H H 8.02 0.01 1 130 696 60 GLN HE21 H 6.52 0.01 2 131 696 60 GLN HE22 H 6.73 0.01 2 132 696 60 GLN N N 119.70 0.10 1 133 696 60 GLN NE2 N 113.10 0.10 1 134 697 61 ARG H H 8.24 0.01 1 135 697 61 ARG N N 118.30 0.10 1 136 698 62 TYR H H 7.93 0.01 1 137 698 62 TYR N N 120.30 0.10 1 138 699 63 TYR H H 8.29 0.01 1 139 699 63 TYR N N 120.10 0.10 1 140 700 64 LEU H H 8.10 0.01 1 141 700 64 LEU N N 119.80 0.10 1 142 701 65 LYS H H 7.75 0.01 1 143 701 65 LYS N N 118.60 0.10 1 144 702 66 HIS H H 7.81 0.01 1 145 702 66 HIS N N 115.70 0.10 1 146 703 67 HIS H H 8.15 0.01 1 147 703 67 HIS N N 117.80 0.10 1 148 704 68 GLY H H 8.27 0.01 1 149 704 68 GLY N N 109.30 0.10 1 150 705 69 LYS H H 8.06 0.01 1 151 705 69 LYS N N 119.80 0.10 1 152 706 70 LEU H H 8.25 0.01 1 153 706 70 LEU N N 123.00 0.10 1 154 707 71 LYS H H 7.83 0.01 1 155 707 71 LYS N N 126.60 0.10 1 stop_ save_