data_11048 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; RecT-bound ssDNA ; _BMRB_accession_number 11048 _BMRB_flat_file_name bmr11048.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' 11047 'Structure of d(TACG) bound to structurally distinct recombinase ttRecO' 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 ecRecT $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 ecRecT _Molecular_mass . _Mol_thiol_state unknown _Details . _Residue_count 269 _Mol_residue_sequence ; MTKQPPIAKADLQKTQGNRA PAAVKNSDVISFINQPSMKE QLAAALPRHMTAERMIRIAT TEIRKVPALGNCDTMSFVSA IVQCSQLGLEPGSALGHAYL LPFGNKNEKSGKKNVQLIIG YRGMIDLARRSGQIASLSAR VVREGDEFSFEFGLDEKLIH RPGENEDAPVTHVYAVARLK DGGTQFEVMTRKQIELVRSL SKAGNNGPWVTHWEEMAKKT AIRRLFKYLPVSIEIQRAVS MDEKEPLTIDPADSSVLTGE YSVIDNSEE ; loop_ _Residue_seq_code _Residue_label 1 MET 2 THR 3 LYS 4 GLN 5 PRO 6 PRO 7 ILE 8 ALA 9 LYS 10 ALA 11 ASP 12 LEU 13 GLN 14 LYS 15 THR 16 GLN 17 GLY 18 ASN 19 ARG 20 ALA 21 PRO 22 ALA 23 ALA 24 VAL 25 LYS 26 ASN 27 SER 28 ASP 29 VAL 30 ILE 31 SER 32 PHE 33 ILE 34 ASN 35 GLN 36 PRO 37 SER 38 MET 39 LYS 40 GLU 41 GLN 42 LEU 43 ALA 44 ALA 45 ALA 46 LEU 47 PRO 48 ARG 49 HIS 50 MET 51 THR 52 ALA 53 GLU 54 ARG 55 MET 56 ILE 57 ARG 58 ILE 59 ALA 60 THR 61 THR 62 GLU 63 ILE 64 ARG 65 LYS 66 VAL 67 PRO 68 ALA 69 LEU 70 GLY 71 ASN 72 CYS 73 ASP 74 THR 75 MET 76 SER 77 PHE 78 VAL 79 SER 80 ALA 81 ILE 82 VAL 83 GLN 84 CYS 85 SER 86 GLN 87 LEU 88 GLY 89 LEU 90 GLU 91 PRO 92 GLY 93 SER 94 ALA 95 LEU 96 GLY 97 HIS 98 ALA 99 TYR 100 LEU 101 LEU 102 PRO 103 PHE 104 GLY 105 ASN 106 LYS 107 ASN 108 GLU 109 LYS 110 SER 111 GLY 112 LYS 113 LYS 114 ASN 115 VAL 116 GLN 117 LEU 118 ILE 119 ILE 120 GLY 121 TYR 122 ARG 123 GLY 124 MET 125 ILE 126 ASP 127 LEU 128 ALA 129 ARG 130 ARG 131 SER 132 GLY 133 GLN 134 ILE 135 ALA 136 SER 137 LEU 138 SER 139 ALA 140 ARG 141 VAL 142 VAL 143 ARG 144 GLU 145 GLY 146 ASP 147 GLU 148 PHE 149 SER 150 PHE 151 GLU 152 PHE 153 GLY 154 LEU 155 ASP 156 GLU 157 LYS 158 LEU 159 ILE 160 HIS 161 ARG 162 PRO 163 GLY 164 GLU 165 ASN 166 GLU 167 ASP 168 ALA 169 PRO 170 VAL 171 THR 172 HIS 173 VAL 174 TYR 175 ALA 176 VAL 177 ALA 178 ARG 179 LEU 180 LYS 181 ASP 182 GLY 183 GLY 184 THR 185 GLN 186 PHE 187 GLU 188 VAL 189 MET 190 THR 191 ARG 192 LYS 193 GLN 194 ILE 195 GLU 196 LEU 197 VAL 198 ARG 199 SER 200 LEU 201 SER 202 LYS 203 ALA 204 GLY 205 ASN 206 ASN 207 GLY 208 PRO 209 TRP 210 VAL 211 THR 212 HIS 213 TRP 214 GLU 215 GLU 216 MET 217 ALA 218 LYS 219 LYS 220 THR 221 ALA 222 ILE 223 ARG 224 ARG 225 LEU 226 PHE 227 LYS 228 TYR 229 LEU 230 PRO 231 VAL 232 SER 233 ILE 234 GLU 235 ILE 236 GLN 237 ARG 238 ALA 239 VAL 240 SER 241 MET 242 ASP 243 GLU 244 LYS 245 GLU 246 PRO 247 LEU 248 THR 249 ILE 250 ASP 251 PRO 252 ALA 253 ASP 254 SER 255 SER 256 VAL 257 LEU 258 THR 259 GLY 260 GLU 261 TYR 262 SER 263 VAL 264 ILE 265 ASP 266 ASN 267 SER 268 GLU 269 GLU 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 DBJ BAA14949 "recombination and repair protein [Escherichia coli str. K12 substr. W3110]" 100.00 269 100.00 100.00 0.00e+00 DBJ BAB35356 "recombinase recT protein [Escherichia coli O157:H7 str. Sakai]" 100.00 269 98.51 99.63 0.00e+00 DBJ BAG76926 "putative phage recombinase [Escherichia coli SE11]" 100.00 269 100.00 100.00 0.00e+00 DBJ BAI25198 "recombination and repair protein [Escherichia coli O26:H11 str. 11368]" 100.00 269 98.51 99.63 0.00e+00 DBJ BAI25911 "putative recombinase [Escherichia coli O26:H11 str. 11368]" 100.00 269 99.26 99.63 0.00e+00 EMBL CAQ31853 "recombinase, DNA renaturation [Escherichia coli BL21(DE3)]" 100.00 269 100.00 100.00 0.00e+00 EMBL CCP96881 "Recombinational DNA repair protein RecT (prophage associated) [Escherichia coli O10:K5(L):H4 str. ATCC 23506]" 100.00 269 100.00 100.00 0.00e+00 EMBL CCP99639 "Recombinational DNA repair protein RecT (prophage associated) [Escherichia coli O5:K4(L):H4 str. ATCC 23502]" 100.00 269 100.00 100.00 0.00e+00 EMBL CDJ71764 "recombination and repair protein RecT [Escherichia coli str. K-12 substr. MC4100]" 100.00 269 100.00 100.00 0.00e+00 EMBL CDK47162 "Recombinational DNA repair protein RecT (prophage associated) [Escherichia coli IS1]" 100.00 269 97.77 99.26 0.00e+00 GB AAA16179 "unknown [Escherichia coli]" 100.00 269 100.00 100.00 0.00e+00 GB AAC74431 "Rac prophage; recombination and repair protein [Escherichia coli str. K-12 substr. MG1655]" 100.00 269 100.00 100.00 0.00e+00 GB AAG56448 "recombinase, DNA renaturation protein encoded by prophage CP-933R [Escherichia coli O157:H7 str. EDL933]" 100.00 269 98.51 99.63 0.00e+00 GB ABJ00798 "recombinational DNA repair protein [Escherichia coli APEC O1]" 100.00 288 100.00 100.00 0.00e+00 GB ACB02570 "Rac prophage; recombination and repair protein [Escherichia coli str. K-12 substr. DH10B]" 100.00 269 100.00 100.00 0.00e+00 REF NP_309960 "recombination and repair protein RecT [Escherichia coli O157:H7 str. Sakai]" 100.00 269 98.51 99.63 0.00e+00 REF NP_415865 "Rac prophage; recombination and repair protein [Escherichia coli str. K-12 substr. MG1655]" 100.00 269 100.00 100.00 0.00e+00 REF WP_000166310 "DNA recombination protein RecT [Escherichia coli]" 100.00 269 97.77 99.63 0.00e+00 REF WP_000166311 "DNA recombination protein RecT [Escherichia coli]" 100.00 269 98.14 99.63 0.00e+00 REF WP_000166312 "DNA recombination protein RecT [Escherichia coli]" 100.00 269 98.14 99.63 0.00e+00 SP P33228 "RecName: Full=Protein RecT; AltName: Full=P33" 100.00 269 100.00 100.00 0.00e+00 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 . 562 Bacteria . . . 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 1 mM 'natural abundance' $entity_2 0.1 mM 'natural abundance' NaCl 100 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' 100 . 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 1.6 0.01 2 3 1 1 DT H2'' H 2.15 0.01 2 4 1 1 DT H3' H 4.57 0.01 1 5 1 1 DT H4' H 3.97 0.01 1 6 1 1 DT H5' H 3.6 0.01 2 7 1 1 DT H5'' H 3.6 0.01 2 8 1 1 DT H6 H 7.28 0.01 1 9 1 1 DT H71 H 1.78 0.01 1 10 1 1 DT H72 H 1.78 0.01 1 11 1 1 DT H73 H 1.78 0.01 1 12 2 2 DA H1' H 6.23 0.01 1 13 2 2 DA H2 H 8.03 0.01 1 14 2 2 DA H2' H 2.77 0.01 1 15 2 2 DA H2'' H 2.68 0.01 1 16 2 2 DA H3' H 4.95 0.01 1 17 2 2 DA H4' H 4.34 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 8.31 0.01 1 21 3 3 DC H1' H 5.99 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 4.73 0.01 1 25 3 3 DC H4' H 4.15 0.01 1 26 3 3 DC H5 H 5.76 0.01 1 27 3 3 DC H5' H 4.02 0.01 2 28 3 3 DC H5'' H 4.02 0.01 2 29 3 3 DC H6 H 7.5 0.01 1 30 4 4 DG H1' H 6.13 0.01 1 31 4 4 DG H2' H 2.7 0.01 1 32 4 4 DG H2'' H 2.43 0.01 1 33 4 4 DG H3' H 4.67 0.01 1 34 4 4 DG H4' H 4.14 0.01 1 35 4 4 DG H5' H 4.05 0.01 2 36 4 4 DG H5'' H 4.05 0.01 2 37 4 4 DG H8 H 7.93 0.01 1 stop_ save_