data_11047 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RecO-bound ssDNA ; _BMRB_accession_number 11047 _BMRB_flat_file_name bmr11047.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 11045 'Structure of d(TACG) bound to structurally distinct recombinase Mhr1p' 11046 'Structure of d(TACG) bound to structurally distinct recombinase hsRad51' 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 ttRecO $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 ttRecO _Molecular_mass . _Mol_thiol_state 'not present' _Details . _Residue_count 229 _Mol_residue_sequence ; MAPAYTGKVERYRLEEGIVV GRKPLPQGDLLLRLVTPRGS LEAVVRKGQRPTGRTGRLSL FHHVRFQLYAKGEGLPTLTQ AELLGRLHGLEAPRRFLLAA FLAELAYRLASPEAAPRIYP LLVSGLRGIAKHEDPLLPLV WAGWRVAKAGGIGPNLEGEG LRLKRGRLGEEGVYLGREGV EALKATLRLPGAQALPHLEG APLNRLFLALKAHAEEALGP LRSAEAIGV ; loop_ _Residue_seq_code _Residue_label 1 MET 2 ALA 3 PRO 4 ALA 5 TYR 6 THR 7 GLY 8 LYS 9 VAL 10 GLU 11 ARG 12 TYR 13 ARG 14 LEU 15 GLU 16 GLU 17 GLY 18 ILE 19 VAL 20 VAL 21 GLY 22 ARG 23 LYS 24 PRO 25 LEU 26 PRO 27 GLN 28 GLY 29 ASP 30 LEU 31 LEU 32 LEU 33 ARG 34 LEU 35 VAL 36 THR 37 PRO 38 ARG 39 GLY 40 SER 41 LEU 42 GLU 43 ALA 44 VAL 45 VAL 46 ARG 47 LYS 48 GLY 49 GLN 50 ARG 51 PRO 52 THR 53 GLY 54 ARG 55 THR 56 GLY 57 ARG 58 LEU 59 SER 60 LEU 61 PHE 62 HIS 63 HIS 64 VAL 65 ARG 66 PHE 67 GLN 68 LEU 69 TYR 70 ALA 71 LYS 72 GLY 73 GLU 74 GLY 75 LEU 76 PRO 77 THR 78 LEU 79 THR 80 GLN 81 ALA 82 GLU 83 LEU 84 LEU 85 GLY 86 ARG 87 LEU 88 HIS 89 GLY 90 LEU 91 GLU 92 ALA 93 PRO 94 ARG 95 ARG 96 PHE 97 LEU 98 LEU 99 ALA 100 ALA 101 PHE 102 LEU 103 ALA 104 GLU 105 LEU 106 ALA 107 TYR 108 ARG 109 LEU 110 ALA 111 SER 112 PRO 113 GLU 114 ALA 115 ALA 116 PRO 117 ARG 118 ILE 119 TYR 120 PRO 121 LEU 122 LEU 123 VAL 124 SER 125 GLY 126 LEU 127 ARG 128 GLY 129 ILE 130 ALA 131 LYS 132 HIS 133 GLU 134 ASP 135 PRO 136 LEU 137 LEU 138 PRO 139 LEU 140 VAL 141 TRP 142 ALA 143 GLY 144 TRP 145 ARG 146 VAL 147 ALA 148 LYS 149 ALA 150 GLY 151 GLY 152 ILE 153 GLY 154 PRO 155 ASN 156 LEU 157 GLU 158 GLY 159 GLU 160 GLY 161 LEU 162 ARG 163 LEU 164 LYS 165 ARG 166 GLY 167 ARG 168 LEU 169 GLY 170 GLU 171 GLU 172 GLY 173 VAL 174 TYR 175 LEU 176 GLY 177 ARG 178 GLU 179 GLY 180 VAL 181 GLU 182 ALA 183 LEU 184 LYS 185 ALA 186 THR 187 LEU 188 ARG 189 LEU 190 PRO 191 GLY 192 ALA 193 GLN 194 ALA 195 LEU 196 PRO 197 HIS 198 LEU 199 GLU 200 GLY 201 ALA 202 PRO 203 LEU 204 ASN 205 ARG 206 LEU 207 PHE 208 LEU 209 ALA 210 LEU 211 LYS 212 ALA 213 HIS 214 ALA 215 GLU 216 GLU 217 ALA 218 LEU 219 GLY 220 PRO 221 LEU 222 ARG 223 SER 224 ALA 225 GLU 226 ALA 227 ILE 228 GLY 229 VAL stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-02-27 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 BMRB 11177 RecO 100.00 229 100.00 100.00 1.73e-151 DBJ BAD70446 "DNA repair protein RecO [Thermus thermophilus HB8]" 100.00 229 100.00 100.00 1.73e-151 GB AAS80606 "hypothetical conserved protein [Thermus thermophilus HB27]" 100.00 291 98.69 99.56 6.82e-150 GB AEG33049 "DNA repair protein RecO [Thermus thermophilus SG0.5JP17-16]" 96.51 221 98.64 99.55 1.50e-142 GB AFH39328 "recombinational DNA repair protein (RecF pathway) [Thermus thermophilus JL-18]" 96.51 221 98.64 99.55 3.99e-143 GB EIA39541 "hypothetical protein RLTM_04716 [Thermus sp. RL]" 95.63 221 98.17 99.54 3.16e-141 REF WP_008632002 "DNA repair protein RecO [Thermus sp. RL]" 95.63 221 98.17 99.54 3.16e-141 REF WP_011228077 "DNA repair protein RecO [Thermus thermophilus]" 100.00 229 100.00 100.00 1.73e-151 REF WP_014510042 "DNA repair protein RecO [Thermus thermophilus]" 96.51 221 98.64 99.55 1.50e-142 REF WP_014629934 "DNA repair protein RecO [Thermus thermophilus]" 96.51 221 98.64 99.55 3.99e-143 REF WP_024119227 "DNA repair protein RecO [Thermus thermophilus]" 96.51 221 98.64 99.55 3.86e-143 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $entity_1 . . . . . . . $entity_2 . 300852 Bacteria . . . HB8 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 pET11a 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 5 mM 'natural abundance' NaCl 150 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 Avance _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_transferred_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name 'transferred NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name TOCSY _Sample_label $sample_1 save_ save_ROESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name 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' 150 . 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' 'transferred NOESY' DQF-COSY TOCSY 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 5.91 0.01 1 2 1 1 DT H2' H 1.60 0.01 2 3 1 1 DT H2'' H 2.15 0.01 2 4 1 1 DT H3' H 4.58 0.01 1 5 1 1 DT H4' H 3.98 0.01 1 6 1 1 DT H5' H 3.61 0.01 2 7 1 1 DT H5'' H 3.61 0.01 2 8 1 1 DT H6 H 7.29 0.01 1 9 1 1 DT H71 H 1.79 0.01 1 10 1 1 DT H72 H 1.79 0.01 1 11 1 1 DT H73 H 1.79 0.01 1 12 2 2 DA H1' H 6.23 0.01 1 13 2 2 DA H2 H 8.04 0.01 1 14 2 2 DA H2' H 2.78 0.01 1 15 2 2 DA H2'' H 2.68 0.01 1 16 2 2 DA H3' H 4.96 0.01 1 17 2 2 DA H4' H 4.35 0.01 1 18 2 2 DA H5' H 4.01 0.01 2 19 2 2 DA H5'' H 4.01 0.01 2 20 2 2 DA H8 H 8.31 0.01 1 21 3 3 DC H1' H 6.00 0.01 1 22 3 3 DC H2' H 1.88 0.01 1 23 3 3 DC H2'' H 2.32 0.01 1 24 3 3 DC H3' H 4.74 0.01 1 25 3 3 DC H4' H 4.16 0.01 1 26 3 3 DC H5 H 5.77 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 7.50 0.01 1 30 4 4 DG H1' H 6.14 0.01 1 31 4 4 DG H2' H 2.70 0.01 1 32 4 4 DG H2'' H 2.45 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 4.06 0.01 2 36 4 4 DG H5'' H 4.06 0.01 2 37 4 4 DG H8 H 7.94 0.01 1 stop_ save_