data_25582 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; structure of a protein ; _BMRB_accession_number 25582 _BMRB_flat_file_name bmr25582.str _Entry_type original _Submission_date 2015-07-27 _Accession_date 2015-07-27 _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 heddi brahim . . 2 Cheong 'Vee Vee' V.V. . 3 Martadinata Herry . . 4 Phan 'Anh Tuan' A.T. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 107 "13C chemical shifts" 76 "15N chemical shifts" 14 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-08-24 update BMRB 'update entry citation' 2015-07-27 original author 'original release' stop_ _Original_release_date 2015-07-27 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26195789 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Heddi Brahim . . 2 Cheong 'Vee Vee' V.V. . 3 Martadinata Herry . . 4 Phan 'Anh Tuan' A.T. . stop_ _Journal_abbreviation 'Proc. Natl. Acad. Sci. U.S.A.' _Journal_volume 112 _Journal_issue 31 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 9608 _Page_last 9613 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Protein and DNA complex' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 "DNA (5'-D(*TP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')" $DNA 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 2360.817 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 20 _Mol_residue_sequence ; SMHPGHLKGREIGMWYAKKQ ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 SER 2 2 MET 3 3 HIS 4 4 PRO 5 5 GLY 6 6 HIS 7 7 LEU 8 8 LYS 9 9 GLY 10 10 ARG 11 11 GLU 12 12 ILE 13 13 GLY 14 14 MET 15 15 TRP 16 16 TYR 17 17 ALA 18 18 LYS 19 19 LYS 20 20 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_DNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common DNA _Molecular_mass 5730.718 _Mol_thiol_state . _Details . _Residue_count 18 _Mol_residue_sequence ; TTGGGTGGGTGGGTGGGT ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 DT 2 2 DT 3 3 DG 4 4 DG 5 5 DG 6 6 DT 7 7 DG 8 8 DG 9 9 DG 10 10 DT 11 11 DG 12 12 DG 13 13 DG 14 14 DT 15 15 DG 16 16 DG 17 17 DG 18 18 DT 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 . . . . . . $DNA . . . . . . 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' . . . . 'pET32 Ek/LIC' $DNA '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 0.1 1 '[U-100% 13C; U-100% 15N]' $DNA . mM 0.1 1 'natural abundance' 'potassium chloride' . mM 10 70 'natural abundance' 'potassium phosphate' . mM 10 20 'natural abundance' $entity_1 . mM 0.1 1 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address Goddard . . 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'chemical shift assignment' 'geometry optimization' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AMX _Field_strength 700 _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-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aliphatic_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_3D_HNCO_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCO' _Sample_label $sample_1 save_ save_3D_CBCA(CO)NH_7 _Saveframe_category NMR_applied_experiment _Experiment_name '3D CBCA(CO)NH' _Sample_label $sample_1 save_ save_3D_HNCACB_8 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNCACB' _Sample_label $sample_1 save_ save_3D_H(CCO)NH_9 _Saveframe_category NMR_applied_experiment _Experiment_name '3D H(CCO)NH' _Sample_label $sample_1 save_ save_3D_HCCH-TOCSY_10 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HCCH-TOCSY' _Sample_label $sample_1 save_ save_3D_HNHA_11 _Saveframe_category NMR_applied_experiment _Experiment_name '3D HNHA' _Sample_label $sample_1 save_ save_3D_1H-13C_NOESY_12 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY' _Sample_label $sample_1 save_ save_3D_1H-15N_NOESY_13 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $sample_1 save_ save_3D_1H-13C_NOESY_aromatic_14 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-13C NOESY aromatic' _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' 0.9 . M pH 6.65 0.05 pH pressure 1 . atm temperature 299 11 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 '2D 1H-15N HSQC' '2D 1H-13C HSQC' '2D 1H-13C HSQC aliphatic' '2D 1H-1H NOESY' '3D HNCO' '3D CBCA(CO)NH' '3D HNCACB' '3D H(CCO)NH' '3D HCCH-TOCSY' '3D 1H-13C NOESY' 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 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 3 3 HIS HA H 4.409 . 1 2 3 3 HIS HB2 H 2.898 . 1 3 3 3 HIS HB3 H 3.225 . 1 4 3 3 HIS HD2 H 6.934 . 1 5 3 3 HIS HE1 H 7.854 . 1 6 3 3 HIS CA C 53.098 . 1 7 3 3 HIS CB C 28.867 . 1 8 3 3 HIS CD2 C 129.936 . 1 9 3 3 HIS CE1 C 134.632 . 1 10 4 4 PRO HA H 3.972 . 1 11 4 4 PRO HB2 H 2.153 . 1 12 4 4 PRO HB3 H 2.153 . 1 13 4 4 PRO HG2 H 1.641 . 1 14 4 4 PRO HG3 H 1.641 . 1 15 4 4 PRO HD2 H 1.684 . 1 16 4 4 PRO HD3 H 1.684 . 1 17 4 4 PRO CA C 60.186 . 1 18 4 4 PRO CB C 29.541 . 1 19 4 4 PRO CG C 24.437 . 1 20 4 4 PRO CD C 45.953 . 1 21 5 5 GLY H H 8.315 . 1 22 5 5 GLY HA2 H 3.691 . 1 23 5 5 GLY HA3 H 3.691 . 1 24 5 5 GLY C C 175.807 . 1 25 5 5 GLY CA C 43.979 . 1 26 5 5 GLY N N 107.940 . 1 27 6 6 HIS H H 7.457 . 1 28 6 6 HIS HA H 4.511 . 1 29 6 6 HIS HB2 H 2.795 . 1 30 6 6 HIS HB3 H 3.180 . 1 31 6 6 HIS HD2 H 6.819 . 1 32 6 6 HIS HE1 H 7.584 . 1 33 6 6 HIS C C 171.192 . 1 34 6 6 HIS CA C 53.404 . 1 35 6 6 HIS CB C 27.292 . 1 36 6 6 HIS CD2 C 130.501 . 1 37 6 6 HIS CE1 C 136.175 . 1 38 6 6 HIS N N 114.183 . 1 39 7 7 LEU H H 6.540 . 1 40 7 7 LEU HA H 3.903 . 1 41 7 7 LEU HB2 H 0.575 . 1 42 7 7 LEU HB3 H 1.294 . 1 43 7 7 LEU HG H 0.721 . 1 44 7 7 LEU HD1 H 0.467 . 1 45 7 7 LEU HD2 H 0.432 . 1 46 7 7 LEU C C 172.872 . 1 47 7 7 LEU CA C 51.661 . 1 48 7 7 LEU CB C 39.808 . 1 49 7 7 LEU CG C 23.515 . 1 50 7 7 LEU CD1 C 23.641 . 1 51 7 7 LEU CD2 C 18.553 . 1 52 7 7 LEU N N 121.536 . 1 53 8 8 LYS H H 8.492 . 1 54 8 8 LYS HA H 4.508 . 1 55 8 8 LYS HB2 H 1.532 . 1 56 8 8 LYS HB3 H 1.637 . 1 57 8 8 LYS HG2 H 1.369 . 1 58 8 8 LYS HG3 H 1.356 . 1 59 8 8 LYS HD2 H 1.613 . 1 60 8 8 LYS HD3 H 1.613 . 1 61 8 8 LYS HE2 H 2.924 . 1 62 8 8 LYS HE3 H 2.944 . 1 63 8 8 LYS C C 172.587 . 1 64 8 8 LYS CA C 51.252 . 1 65 8 8 LYS CB C 33.375 . 1 66 8 8 LYS CG C 21.479 . 1 67 8 8 LYS CD C 25.920 . 1 68 8 8 LYS CE C 38.986 . 1 69 8 8 LYS N N 119.261 . 1 70 9 9 GLY H H 8.694 . 1 71 9 9 GLY HA2 H 3.756 . 1 72 9 9 GLY HA3 H 3.756 . 1 73 9 9 GLY C C 174.090 . 1 74 9 9 GLY CA C 43.824 . 1 75 9 9 GLY N N 112.295 . 1 76 10 10 ARG H H 8.798 . 1 77 10 10 ARG HA H 3.036 . 1 78 10 10 ARG HB2 H 1.007 . 1 79 10 10 ARG HB3 H 1.239 . 1 80 10 10 ARG HG2 H 0.444 . 1 81 10 10 ARG HG3 H 1.300 . 1 82 10 10 ARG HD2 H 3.000 . 1 83 10 10 ARG HD3 H 3.000 . 1 84 10 10 ARG C C 171.915 . 1 85 10 10 ARG CA C 55.701 . 1 86 10 10 ARG CB C 26.571 . 1 87 10 10 ARG CG C 24.450 . 1 88 10 10 ARG CD C 40.345 . 1 89 10 10 ARG N N 126.817 . 1 90 11 11 GLU H H 7.453 . 1 91 11 11 GLU HA H 3.640 . 1 92 11 11 GLU HB2 H 1.884 . 1 93 11 11 GLU HB3 H 1.974 . 1 94 11 11 GLU HG2 H 2.098 . 1 95 11 11 GLU HG3 H 2.365 . 1 96 11 11 GLU C C 173.276 . 1 97 11 11 GLU CA C 55.429 . 1 98 11 11 GLU CB C 27.765 . 1 99 11 11 GLU CG C 33.367 . 1 100 11 11 GLU N N 113.440 . 1 101 12 12 ILE H H 7.499 . 1 102 12 12 ILE HA H 2.869 . 1 103 12 12 ILE HB H 0.975 . 1 104 12 12 ILE HG12 H -0.158 . 1 105 12 12 ILE HG13 H 0.655 . 1 106 12 12 ILE HG2 H -0.246 . 1 107 12 12 ILE HD1 H 0.067 . 1 108 12 12 ILE C C 176.838 . 1 109 12 12 ILE CA C 62.604 . 1 110 12 12 ILE CB C 34.803 . 1 111 12 12 ILE CG1 C 25.819 . 1 112 12 12 ILE CG2 C 12.553 . 1 113 12 12 ILE CD1 C 10.092 . 1 114 12 12 ILE N N 118.236 . 1 115 13 13 GLY H H 6.135 . 1 116 13 13 GLY HA2 H 4.366 . 1 117 13 13 GLY HA3 H 4.348 . 1 118 13 13 GLY C C 174.111 . 1 119 13 13 GLY CA C 45.606 . 1 120 13 13 GLY N N 104.389 . 1 121 14 14 MET H H 7.977 . 1 122 14 14 MET HA H 3.952 . 1 123 14 14 MET HB2 H 1.647 . 1 124 14 14 MET HB3 H 2.166 . 1 125 14 14 MET HG2 H 1.858 . 1 126 14 14 MET HG3 H 2.537 . 1 127 14 14 MET HE H 1.703 . 1 128 14 14 MET CA C 53.002 . 1 129 14 14 MET CB C 30.242 . 1 130 14 14 MET CG C 30.178 . 1 131 14 14 MET CE C 15.852 . 1 132 14 14 MET N N 114.865 . 1 133 15 15 TRP H H 7.489 . 1 134 15 15 TRP HA H 3.725 . 1 135 15 15 TRP HB2 H 2.698 . 1 136 15 15 TRP HB3 H 2.950 . 1 137 15 15 TRP HE1 H 10.107 . 1 138 15 15 TRP HE3 H 6.857 . 1 139 15 15 TRP HZ2 H 7.221 . 1 140 15 15 TRP HZ3 H 6.377 . 1 141 15 15 TRP HH2 H 6.834 . 1 142 15 15 TRP C C 175.377 . 1 143 15 15 TRP CA C 59.311 . 1 144 15 15 TRP CB C 25.410 . 1 145 15 15 TRP CE3 C 115.069 . 1 146 15 15 TRP CZ2 C 111.157 . 1 147 15 15 TRP CZ3 C 119.615 . 1 148 15 15 TRP CH2 C 120.991 . 1 149 15 15 TRP N N 122.784 . 1 150 16 16 TYR HE1 H 6.655 . 1 151 16 16 TYR HE2 H 6.655 . 1 152 16 16 TYR CE1 C 116.525 . 1 153 16 16 TYR CE2 C 116.525 . 1 154 17 17 ALA HA H 3.773 . 1 155 17 17 ALA HB H 0.696 . 1 156 17 17 ALA CA C 51.092 . 1 157 17 17 ALA CB C 15.083 . 1 158 18 18 LYS H H 7.246 . 1 159 18 18 LYS HA H 4.002 . 1 160 18 18 LYS HB2 H 1.583 . 1 161 18 18 LYS HB3 H 1.583 . 1 162 18 18 LYS HG2 H 1.261 . 1 163 18 18 LYS HG3 H 1.261 . 1 164 18 18 LYS HD2 H 1.569 . 1 165 18 18 LYS HD3 H 1.569 . 1 166 18 18 LYS HE2 H 2.687 . 1 167 18 18 LYS HE3 H 2.687 . 1 168 18 18 LYS C C 175.108 . 1 169 18 18 LYS CA C 52.995 . 1 170 18 18 LYS CB C 28.686 . 1 171 18 18 LYS CG C 21.532 . 1 172 18 18 LYS CD C 25.826 . 1 173 18 18 LYS CE C 38.913 . 1 174 18 18 LYS N N 115.668 . 1 175 19 19 LYS H H 7.841 . 1 176 19 19 LYS HA H 3.858 . 1 177 19 19 LYS HB2 H 1.542 . 1 178 19 19 LYS HB3 H 1.542 . 1 179 19 19 LYS HG2 H 1.215 . 1 180 19 19 LYS HG3 H 1.215 . 1 181 19 19 LYS HD2 H 1.483 . 1 182 19 19 LYS HD3 H 1.483 . 1 183 19 19 LYS HE2 H 2.807 . 1 184 19 19 LYS HE3 H 2.807 . 1 185 19 19 LYS C C 172.881 . 1 186 19 19 LYS CA C 53.325 . 1 187 19 19 LYS CB C 29.238 . 1 188 19 19 LYS CG C 21.511 . 1 189 19 19 LYS CD C 25.398 . 1 190 19 19 LYS CE C 39.354 . 1 191 19 19 LYS N N 121.064 . 1 192 20 20 GLN H H 7.699 . 1 193 20 20 GLN HA H 3.935 . 1 194 20 20 GLN C C 172.759 . 1 195 20 20 GLN CA C 53.213 . 1 196 20 20 GLN CB C 26.879 . 1 197 20 20 GLN N N 125.683 . 1 stop_ save_