data_11045 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Mhr1p-bound ssDNA ; _BMRB_accession_number 11045 _BMRB_flat_file_name bmr11045.str _Entry_type original _Submission_date 2008-05-15 _Accession_date 2008-05-15 _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 Shibata Takehiko . . 2 Ito Yutaka . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 37 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-09-20 update BMRB 'update sequence to DNA' 2010-01-25 update BMRB 'complete entry citation' 2009-10-15 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 11046 'Structure of d(TACG) bound to structurally distinct recombinase hsRad51' 11047 'Structure of d(TACG) bound to structurally distinct recombinase ttRecO' 11048 'Structure of d(TACG) bound to structurally distinct recombinase ecRecT' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'A non-canonical DNA structure enables homologous recombination in various genetic systems.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19729448 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Masuda Tokiha . . 2 Ito Yutaka . . 3 Terada Tohru . . 4 Shibata Takehiko . . 5 Mikawa Tsutomu . . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 284 _Journal_issue 44 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 30230 _Page_last 30239 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name "5'-D(*DTP*DAP*DCP*DG)-3' 10 structures" _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 1' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 2' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 3' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 4' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 5' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 6' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 7' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 8' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 9' $entity_1 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 10' $entity_1 Mhr1p $entity_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_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class DNA _Name_common 'DNA (5'-D(*DTP*DAP*DCP*DG)-3')' _Molecular_mass 1231.30 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 4 _Mol_residue_sequence TACG loop_ _Residue_seq_code _Residue_label 1 DT 2 DA 3 DC 4 DG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ save_entity_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Mhr1p _Molecular_mass . _Mol_thiol_state 'all free' _Details . _Residue_count 226 _Mol_residue_sequence ; MKVNHSISRFRPASWFEKTK IIPPQVYIFRNLEYGQVLYS QFPNFSQTQVDKLFVRPNWS NRKPSLRRDIWKCMCVVNLQ NYKQSVHLYQNLCRLRYLRD VAQRKESDKLRKKDSNGHVW YSGQYRPTYCQEAVADLRES LLKVFENATPAEKQTVPAKK PSIYWEDPWRMGDKDKHWNY DVFNALGLEHKLIQRVGNIA REESVILKELAKLESHPTEQ TEVSSQ ; loop_ _Residue_seq_code _Residue_label 1 MET 2 LYS 3 VAL 4 ASN 5 HIS 6 SER 7 ILE 8 SER 9 ARG 10 PHE 11 ARG 12 PRO 13 ALA 14 SER 15 TRP 16 PHE 17 GLU 18 LYS 19 THR 20 LYS 21 ILE 22 ILE 23 PRO 24 PRO 25 GLN 26 VAL 27 TYR 28 ILE 29 PHE 30 ARG 31 ASN 32 LEU 33 GLU 34 TYR 35 GLY 36 GLN 37 VAL 38 LEU 39 TYR 40 SER 41 GLN 42 PHE 43 PRO 44 ASN 45 PHE 46 SER 47 GLN 48 THR 49 GLN 50 VAL 51 ASP 52 LYS 53 LEU 54 PHE 55 VAL 56 ARG 57 PRO 58 ASN 59 TRP 60 SER 61 ASN 62 ARG 63 LYS 64 PRO 65 SER 66 LEU 67 ARG 68 ARG 69 ASP 70 ILE 71 TRP 72 LYS 73 CYS 74 MET 75 CYS 76 VAL 77 VAL 78 ASN 79 LEU 80 GLN 81 ASN 82 TYR 83 LYS 84 GLN 85 SER 86 VAL 87 HIS 88 LEU 89 TYR 90 GLN 91 ASN 92 LEU 93 CYS 94 ARG 95 LEU 96 ARG 97 TYR 98 LEU 99 ARG 100 ASP 101 VAL 102 ALA 103 GLN 104 ARG 105 LYS 106 GLU 107 SER 108 ASP 109 LYS 110 LEU 111 ARG 112 LYS 113 LYS 114 ASP 115 SER 116 ASN 117 GLY 118 HIS 119 VAL 120 TRP 121 TYR 122 SER 123 GLY 124 GLN 125 TYR 126 ARG 127 PRO 128 THR 129 TYR 130 CYS 131 GLN 132 GLU 133 ALA 134 VAL 135 ALA 136 ASP 137 LEU 138 ARG 139 GLU 140 SER 141 LEU 142 LEU 143 LYS 144 VAL 145 PHE 146 GLU 147 ASN 148 ALA 149 THR 150 PRO 151 ALA 152 GLU 153 LYS 154 GLN 155 THR 156 VAL 157 PRO 158 ALA 159 LYS 160 LYS 161 PRO 162 SER 163 ILE 164 TYR 165 TRP 166 GLU 167 ASP 168 PRO 169 TRP 170 ARG 171 MET 172 GLY 173 ASP 174 LYS 175 ASP 176 LYS 177 HIS 178 TRP 179 ASN 180 TYR 181 ASP 182 VAL 183 PHE 184 ASN 185 ALA 186 LEU 187 GLY 188 LEU 189 GLU 190 HIS 191 LYS 192 LEU 193 ILE 194 GLN 195 ARG 196 VAL 197 GLY 198 ASN 199 ILE 200 ALA 201 ARG 202 GLU 203 GLU 204 SER 205 VAL 206 ILE 207 LEU 208 LYS 209 GLU 210 LEU 211 ALA 212 LYS 213 LEU 214 GLU 215 SER 216 HIS 217 PRO 218 THR 219 GLU 220 GLN 221 THR 222 GLU 223 VAL 224 SER 225 SER 226 GLN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-07-15 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 1VW4 "Structure Of The Yeast Mitochondrial Large Ribosomal Subunit" 100.00 226 100.00 100.00 5.28e-167 DBJ BAA88081 "MHR1 [Saccharomyces cerevisiae]" 100.00 226 100.00 100.00 5.28e-167 DBJ GAA22516 "K7_Mhr1p [Saccharomyces cerevisiae Kyokai no. 7]" 100.00 226 100.00 100.00 5.28e-167 EMBL CAY78797 "Mhr1p [Saccharomyces cerevisiae EC1118]" 100.00 226 98.67 98.67 1.38e-164 GB AAB64732 "Ydr296wp [Saccharomyces cerevisiae]" 100.00 226 100.00 100.00 5.28e-167 GB AAS56061 "YDR296W [Saccharomyces cerevisiae]" 100.00 226 100.00 100.00 5.28e-167 GB AHY75269 "Mhr1p [Saccharomyces cerevisiae YJM993]" 100.00 226 99.12 99.12 4.15e-165 GB AJP37996 "Mhr1p [Saccharomyces cerevisiae YJM1078]" 100.00 226 99.12 99.12 4.15e-165 GB AJU58119 "Mhr1p [Saccharomyces cerevisiae YJM189]" 100.00 226 98.67 98.67 2.67e-164 REF NP_010582 "Mhr1p [Saccharomyces cerevisiae S288c]" 100.00 226 100.00 100.00 5.28e-167 SP Q06630 "RecName: Full=Mitochondrial homologous recombination protein 1; AltName: Full=Cross-linked transcription component 1" 100.00 226 100.00 100.00 5.28e-167 TPG DAA12135 "TPA: Mhr1p [Saccharomyces cerevisiae S288c]" 100.00 226 100.00 100.00 5.28e-167 stop_ 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 . . . . . . $entity_2 'baker's yeast' 4932 Eukaryota Fungi . . 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 $entity_1 'obtained from a vendor' . . . . . . $entity_2 'recombinant technology' . . . BL21(DE3) plasmid pET14b 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 $entity_1 0.5 mM 'natural abundance' $entity_2 0.05 mM 'natural abundance' MgCl2 6.7 mM 'natural abundance' NaCl 50 mM 'natural abundance' D2O 100 % . 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 processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_transferred_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H transferred NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _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 temperature 298 . K pH 7.1 . pH pressure 1 . atm 'ionic strength' 50 . mM 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 0.0 . indirect . . . 1.0 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-1H NOESY' '2D 1H-1H transferred NOESY' '2D 1H-1H DQF-COSY' '2D 1H-1H TOCSY' '2D 1H-1H ROESY' 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 'DNA (5'-D(*DTP*DAP*DCP*DG)-3') 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 1 DT H1' H 5.93 0.01 1 2 1 1 DT H2' H 1.64 0.01 2 3 1 1 DT H2'' H 2.18 0.01 2 4 1 1 DT H3' H 4.60 0.01 1 5 1 1 DT H4' H 4.00 0.01 1 6 1 1 DT H5' H 3.63 0.01 2 7 1 1 DT H5'' H 3.63 0.01 2 8 1 1 DT H6 H 7.31 0.01 1 9 1 1 DT H71 H 1.81 0.01 1 10 1 1 DT H72 H 1.81 0.01 1 11 1 1 DT H73 H 1.81 0.01 1 12 2 2 DA H1' H 6.26 0.01 1 13 2 2 DA H2 H 8.07 0.01 1 14 2 2 DA H2' H 2.80 0.01 1 15 2 2 DA H2'' H 2.70 0.01 1 16 2 2 DA H3' H 4.98 0.01 1 17 2 2 DA H4' H 4.37 0.01 1 18 2 2 DA H5' H 4.02 0.01 2 19 2 2 DA H5'' H 4.02 0.01 2 20 2 2 DA H8 H 8.33 0.01 1 21 3 3 DC H1' H 6.06 0.01 1 22 3 3 DC H2' H 1.92 0.01 1 23 3 3 DC H2'' H 2.35 0.01 1 24 3 3 DC H3' H 4.75 0.01 1 25 3 3 DC H4' H 4.18 0.01 1 26 3 3 DC H5 H 5.79 0.01 1 27 3 3 DC H5' H 4.04 0.01 2 28 3 3 DC H5'' H 4.04 0.01 2 29 3 3 DC H6 H 7.53 0.01 1 30 4 4 DG H1' H 6.15 0.01 1 31 4 4 DG H2' H 2.71 0.01 1 32 4 4 DG H2'' H 2.44 0.01 1 33 4 4 DG H3' H 4.68 0.01 1 34 4 4 DG H4' H 4.16 0.01 1 35 4 4 DG H5' H 4.07 0.01 2 36 4 4 DG H5'' H 4.07 0.01 2 37 4 4 DG H8 H 7.95 0.01 1 stop_ save_