data_19540 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; haddock model of MyT1 F4F5 - DNA complex ; _BMRB_accession_number 19540 _BMRB_flat_file_name bmr19540.str _Entry_type original _Submission_date 2013-10-08 _Accession_date 2013-10-08 _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 Gamsjaeger Roland . . 2 O'Connell Mitchell R . 3 Cubeddu Liza . . 4 Shepherd Nicholas E. . 5 Lowry Jason A. . 6 Kwan Ann H. . 7 Vandevenne Marylene . . 8 Swanton Michael K. . 9 Matthews Jacqueline M. . 10 Mackay Joel P. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 51 "13C chemical shifts" 115 "15N chemical shifts" 51 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-01-31 update BMRB 'update entry citation' 2013-11-04 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24097990 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gamsjaeger Roland . . 2 Cubeddu Mitchell R. . 3 Shepherd Liza . . 4 Lowry Nicholas E. . 5 Kwan Jason A. . 6 Vandevenne Ann H. . 7 Swanton Marylene . . 8 Matthews Michael K. . 9 Mackay Jacqueline M. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 288 _Journal_issue 49 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 35180 _Page_last 35191 _Year 2013 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'MyT1 F4F5 - DNA complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Myelin transcription factor 1' $entity_1 'DNA (26-MER)' $DNA_26_mer 'ZINC ION_1' $entity_ZN 'ZINC ION_2' $entity_ZN 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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity_1 _Molecular_mass 65.380 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 93 _Mol_residue_sequence ; GPLGSFDIKKELLTCPTPGC DGSGHITGNYASHRSLSGCP LADKSLRNLMAAHSADLKCP TPGCDGSGHITGNYASHRSL SGCPRAKKSGLRV ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 788 GLY 2 789 PRO 3 790 LEU 4 791 GLY 5 792 SER 6 793 PHE 7 794 ASP 8 795 ILE 9 796 LYS 10 797 LYS 11 798 GLU 12 799 LEU 13 800 LEU 14 801 THR 15 802 CYS 16 803 PRO 17 804 THR 18 805 PRO 19 806 GLY 20 807 CYS 21 808 ASP 22 809 GLY 23 810 SER 24 811 GLY 25 812 HIS 26 813 ILE 27 814 THR 28 815 GLY 29 816 ASN 30 817 TYR 31 818 ALA 32 819 SER 33 820 HIS 34 821 ARG 35 822 SER 36 823 LEU 37 824 SER 38 825 GLY 39 826 CYS 40 827 PRO 41 828 LEU 42 829 ALA 43 830 ASP 44 831 LYS 45 832 SER 46 833 LEU 47 834 ARG 48 835 ASN 49 836 LEU 50 837 MET 51 838 ALA 52 839 ALA 53 840 HIS 54 841 SER 55 842 ALA 56 843 ASP 57 844 LEU 58 845 LYS 59 846 CYS 60 847 PRO 61 848 THR 62 849 PRO 63 850 GLY 64 851 CYS 65 852 ASP 66 853 GLY 67 854 SER 68 855 GLY 69 856 HIS 70 857 ILE 71 858 THR 72 859 GLY 73 860 ASN 74 861 TYR 75 862 ALA 76 863 SER 77 864 HIS 78 865 ARG 79 866 SER 80 867 LEU 81 868 SER 82 869 GLY 83 870 CYS 84 871 PRO 85 872 ARG 86 873 ALA 87 874 LYS 88 875 LYS 89 876 SER 90 877 GLY 91 878 LEU 92 879 ARG 93 880 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-09 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2MF8 "Haddock Model Of Myt1 F4f5 - Dna Complex" 100.00 93 100.00 100.00 1.95e-58 stop_ save_ save_DNA_26_mer _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA_26_mer _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 26 _Mol_residue_sequence ; ACCGAAAGTTCACGTGAACT TTCGGT ; loop_ _Residue_seq_code _Residue_label 1 DA 2 DC 3 DC 4 DG 5 DA 6 DA 7 DA 8 DG 9 DT 10 DT 11 DC 12 DA 13 DC 14 DG 15 DT 16 DG 17 DA 18 DA 19 DC 20 DT 21 DT 22 DT 23 DC 24 DG 25 DG 26 DT stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common "entity_ZN (ZINC ION)" _BMRB_code ZN _PDB_code ZN _Molecular_mass 65.409 _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 ZN ZN ZN . 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 '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_name $entity_1 'recombinant technology' . . . . pGEX-6P $DNA_26_mer '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $entity_1 . mM 0.2 1.0 '[U-13C; U-15N]' $DNA_26_mer . mM 0.2 1.0 'natural abundance' phosphate 10 mM . . 'natural abundance' NaCl 50 mM . . 'natural abundance' DTT 1 mM . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_HADDOCK _Saveframe_category software _Name HADDOCK _Version . loop_ _Vendor _Address _Electronic_address 'Alexandre Bonvin' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_Avance_600 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_Avance_800 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _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_1 save_ save_3D_CBCA(CO)NH_3 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCACB_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_HNCO_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_HN(CA)CO_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HN(CA)CO' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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' 60 . mM pH 7.2 . 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 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 '3D CBCA(CO)NH' '3D HNCACB' '3D HNCO' '3D HN(CA)CO' 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 'Myelin transcription factor 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 1 799 12 LEU H H 8.184 . 1 2 799 12 LEU CA C 54.815 . 1 3 799 12 LEU CB C 42.525 . 1 4 799 12 LEU N N 124.209 . 1 5 800 13 LEU H H 8.284 . 1 6 800 13 LEU CA C 55.522 . 1 7 800 13 LEU CB C 41.945 . 1 8 800 13 LEU N N 122.909 . 1 9 801 14 THR H H 7.916 . 1 10 801 14 THR CA C 59.411 . 1 11 801 14 THR CB C 71.888 . 1 12 801 14 THR N N 112.617 . 1 13 802 15 CYS H H 8.515 . 1 14 802 15 CYS CA C 57.598 . 1 15 802 15 CYS CB C 29.644 . 1 16 802 15 CYS N N 125.623 . 1 17 803 16 PRO CA C 63.412 . 1 18 803 16 PRO CB C 32.274 . 1 19 804 17 THR H H 9.774 . 1 20 804 17 THR CA C 61.828 . 1 21 804 17 THR CB C 67.788 . 1 22 804 17 THR N N 129.174 . 1 23 805 18 PRO CA C 64.154 . 1 24 805 18 PRO CB C 31.641 . 1 25 806 19 GLY H H 8.777 . 1 26 806 19 GLY CA C 45.342 . 1 27 806 19 GLY N N 112.562 . 1 28 807 20 CYS H H 7.863 . 1 29 807 20 CYS CA C 59.687 . 1 30 807 20 CYS CB C 31.447 . 1 31 807 20 CYS N N 123.196 . 1 32 808 21 ASP H H 8.412 . 1 33 808 21 ASP CA C 53.266 . 1 34 808 21 ASP CB C 40.743 . 1 35 808 21 ASP N N 129.423 . 1 36 809 22 GLY H H 10.012 . 1 37 809 22 GLY CA C 44.862 . 1 38 809 22 GLY N N 115.508 . 1 39 810 23 SER H H 8.212 . 1 40 810 23 SER CA C 59.834 . 1 41 810 23 SER CB C 64.722 . 1 42 810 23 SER N N 115.696 . 1 43 811 24 GLY H H 7.973 . 1 44 811 24 GLY CA C 44.882 . 1 45 811 24 GLY N N 108.285 . 1 46 812 25 HIS H H 8.517 . 1 47 812 25 HIS CA C 59.200 . 1 48 812 25 HIS CB C 36.415 . 1 49 812 25 HIS N N 116.608 . 1 50 813 26 ILE H H 8.029 . 1 51 813 26 ILE CA C 63.829 . 1 52 813 26 ILE CB C 38.198 . 1 53 813 26 ILE N N 131.617 . 1 54 814 27 THR H H 9.480 . 1 55 814 27 THR CA C 63.630 . 1 56 814 27 THR CB C 72.617 . 1 57 814 27 THR N N 113.984 . 1 58 815 28 GLY H H 8.070 . 1 59 815 28 GLY CA C 45.693 . 1 60 815 28 GLY N N 106.672 . 1 61 816 29 ASN H H 8.034 . 1 62 816 29 ASN CA C 53.481 . 1 63 816 29 ASN CB C 39.091 . 1 64 816 29 ASN N N 115.952 . 1 65 817 30 TYR H H 6.480 . 1 66 817 30 TYR CA C 56.361 . 1 67 817 30 TYR CB C 41.522 . 1 68 817 30 TYR N N 113.870 . 1 69 818 31 ALA CA C 53.406 . 1 70 818 31 ALA CB C 20.074 . 1 71 819 32 SER H H 8.102 . 1 72 819 32 SER CA C 58.033 . 1 73 819 32 SER CB C 66.571 . 1 74 819 32 SER N N 115.473 . 1 75 820 33 HIS H H 8.712 . 1 76 820 33 HIS CA C 55.787 . 1 77 820 33 HIS CB C 32.236 . 1 78 820 33 HIS N N 110.346 . 1 79 821 34 ARG CA C 54.315 . 1 80 821 34 ARG CB C 29.700 . 1 81 822 35 SER H H 7.572 . 1 82 822 35 SER CA C 57.084 . 1 83 822 35 SER CB C 66.534 . 1 84 822 35 SER N N 112.336 . 1 85 823 36 LEU H H 8.951 . 1 86 823 36 LEU CA C 57.465 . 1 87 823 36 LEU N N 121.821 . 1 88 824 37 SER CA C 61.148 . 1 89 824 37 SER CB C 62.521 . 1 90 825 38 GLY H H 7.379 . 1 91 825 38 GLY CA C 44.707 . 1 92 825 38 GLY N N 107.480 . 1 93 826 39 CYS H H 7.278 . 1 94 826 39 CYS CA C 57.619 . 1 95 826 39 CYS CB C 30.346 . 1 96 826 39 CYS N N 126.098 . 1 97 829 42 ALA H H 7.153 . 1 98 829 42 ALA CA C 52.777 . 1 99 829 42 ALA CB C 19.462 . 1 100 829 42 ALA N N 124.342 . 1 101 830 43 ASP H H 8.376 . 1 102 830 43 ASP CA C 54.533 . 1 103 830 43 ASP CB C 40.725 . 1 104 830 43 ASP N N 119.463 . 1 105 837 50 MET H H 8.226 . 1 106 837 50 MET CA C 56.391 . 1 107 837 50 MET CB C 32.439 . 1 108 837 50 MET N N 120.040 . 1 109 841 54 SER CA C 58.593 . 1 110 841 54 SER CB C 63.979 . 1 111 842 55 ALA H H 8.560 . 1 112 842 55 ALA CA C 52.686 . 1 113 842 55 ALA CB C 19.422 . 1 114 842 55 ALA N N 126.567 . 1 115 843 56 ASP H H 8.339 . 1 116 843 56 ASP CA C 54.519 . 1 117 843 56 ASP CB C 40.757 . 1 118 843 56 ASP N N 119.351 . 1 119 844 57 LEU CA C 55.276 . 1 120 844 57 LEU CB C 41.761 . 1 121 845 58 LYS H H 7.887 . 1 122 845 58 LYS CA C 54.424 . 1 123 845 58 LYS CB C 35.165 . 1 124 845 58 LYS N N 120.944 . 1 125 846 59 CYS H H 8.590 . 1 126 846 59 CYS N N 125.004 . 1 127 847 60 PRO CA C 63.412 . 1 128 847 60 PRO CB C 32.274 . 1 129 848 61 THR H H 9.774 . 1 130 848 61 THR CA C 61.828 . 1 131 848 61 THR CB C 67.788 . 1 132 848 61 THR N N 129.174 . 1 133 849 62 PRO CA C 64.140 . 1 134 849 62 PRO CB C 31.672 . 1 135 850 63 GLY H H 8.797 . 1 136 850 63 GLY CA C 45.480 . 1 137 850 63 GLY N N 112.595 . 1 138 851 64 CYS H H 7.911 . 1 139 851 64 CYS CA C 60.062 . 1 140 851 64 CYS CB C 30.929 . 1 141 851 64 CYS N N 123.279 . 1 142 852 65 ASP H H 8.463 . 1 143 852 65 ASP CA C 53.334 . 1 144 852 65 ASP CB C 40.673 . 1 145 852 65 ASP N N 129.716 . 1 146 853 66 GLY H H 9.833 . 1 147 853 66 GLY CA C 44.919 . 1 148 853 66 GLY N N 114.887 . 1 149 854 67 SER H H 8.321 . 1 150 854 67 SER CA C 59.689 . 1 151 854 67 SER CB C 64.858 . 1 152 854 67 SER N N 115.725 . 1 153 855 68 GLY H H 8.062 . 1 154 855 68 GLY CA C 44.839 . 1 155 855 68 GLY N N 108.446 . 1 156 856 69 HIS H H 8.518 . 1 157 856 69 HIS CA C 59.242 . 1 158 856 69 HIS CB C 36.379 . 1 159 856 69 HIS N N 116.620 . 1 160 857 70 ILE H H 8.024 . 1 161 857 70 ILE CA C 63.951 . 1 162 857 70 ILE CB C 38.221 . 1 163 857 70 ILE N N 131.717 . 1 164 858 71 THR H H 9.509 . 1 165 858 71 THR CA C 63.636 . 1 166 858 71 THR CB C 72.659 . 1 167 858 71 THR N N 114.038 . 1 168 859 72 GLY H H 8.126 . 1 169 859 72 GLY CA C 45.724 . 1 170 859 72 GLY N N 106.708 . 1 171 860 73 ASN H H 8.033 . 1 172 860 73 ASN CA C 53.481 . 1 173 860 73 ASN CB C 39.091 . 1 174 860 73 ASN N N 115.956 . 1 175 861 74 TYR H H 6.493 . 1 176 861 74 TYR CA C 56.361 . 1 177 861 74 TYR CB C 41.490 . 1 178 861 74 TYR N N 113.870 . 1 179 862 75 ALA CA C 53.393 . 1 180 862 75 ALA CB C 20.058 . 1 181 863 76 SER H H 8.115 . 1 182 863 76 SER CA C 58.051 . 1 183 863 76 SER CB C 66.561 . 1 184 863 76 SER N N 115.433 . 1 185 864 77 HIS H H 8.915 . 1 186 864 77 HIS CA C 55.840 . 1 187 864 77 HIS CB C 32.396 . 1 188 864 77 HIS N N 110.288 . 1 189 865 78 ARG CA C 54.306 . 1 190 865 78 ARG CB C 29.695 . 1 191 866 79 SER H H 7.555 . 1 192 866 79 SER CA C 57.082 . 1 193 866 79 SER CB C 66.513 . 1 194 866 79 SER N N 112.021 . 1 195 867 80 LEU H H 9.026 . 1 196 867 80 LEU CA C 57.354 . 1 197 867 80 LEU CB C 41.962 . 1 198 867 80 LEU N N 122.191 . 1 199 868 81 SER CA C 61.148 . 1 200 868 81 SER CB C 62.521 . 1 201 869 82 GLY H H 7.379 . 1 202 869 82 GLY CA C 44.688 . 1 203 869 82 GLY N N 107.483 . 1 204 870 83 CYS H H 7.364 . 1 205 870 83 CYS CA C 57.603 . 1 206 870 83 CYS CB C 30.574 . 1 207 870 83 CYS N N 126.309 . 1 208 871 84 PRO CA C 63.695 . 1 209 871 84 PRO CB C 32.317 . 1 210 872 85 ARG H H 8.809 . 1 211 872 85 ARG CA C 55.541 . 1 212 872 85 ARG CB C 30.471 . 1 213 872 85 ARG N N 122.223 . 1 214 873 86 ALA H H 7.290 . 1 215 873 86 ALA CA C 52.919 . 1 216 873 86 ALA CB C 19.631 . 1 217 873 86 ALA N N 124.469 . 1 stop_ save_