data_19986 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of Xenopus RecQ4 zinc knuckle ; _BMRB_accession_number 19986 _BMRB_flat_file_name bmr19986.str _Entry_type original _Submission_date 2014-05-23 _Accession_date 2014-05-23 _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 Zucchelli Chiara . . 2 Marino Francesca . . 3 Mojumdar Aditya . . 4 Onesti Silvia . . 5 Musco Giovanna . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 132 "13C chemical shifts" 43 "15N chemical shifts" 21 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-08-03 original BMRB . stop_ _Original_release_date 2015-08-03 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; A novel RNA/DNA binding motif in the N-terminal domain of RecQ4 ; _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Marino Francesca . . 2 Mojumdar Aditya . . 3 Zucchelli Chiara . . 4 Musco Giovanna . . 5 Buratti Emanuele . . 6 Vindigni Alessandro . . 7 Onesti Silvia . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Xenopus RecQ4 zinc knuckle' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RecQ4_zinc_knuckle $RecQ4_zinc_knuckle 'ZINC ION' $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_RecQ4_zinc_knuckle _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common RecQ4_zinc_knuckle _Molecular_mass 2613.915 _Mol_thiol_state 'all other bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 25 _Mol_residue_sequence ; NRSGDTCFRCGGMGHWASQC PGSVP ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 ASN 2 2 ARG 3 3 SER 4 4 GLY 5 5 ASP 6 6 THR 7 7 CYS 8 8 PHE 9 9 ARG 10 10 CYS 11 11 GLY 12 12 GLY 13 13 MET 14 14 GLY 15 15 HIS 16 16 TRP 17 17 ALA 18 18 SER 19 19 GLN 20 20 CYS 21 21 PRO 22 22 GLY 23 23 SER 24 24 VAL 25 25 PRO stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-25 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 2MPJ "Nmr Structure Of Xenopus Recq4 Zinc Knuckle" 100.00 25 100.00 100.00 8.27e-09 DBJ BAE48358 "RecQ4 protein [Xenopus laevis]" 100.00 1503 100.00 100.00 2.25e-10 GB AAI61707 "Rts protein [Xenopus laevis]" 100.00 1504 100.00 100.00 2.47e-10 GB AAY89585 "RECQL4-helicase-like protein [Xenopus laevis]" 100.00 1500 100.00 100.00 2.04e-10 REF NP_001089101 "RECQL4-helicase-like protein [Xenopus laevis]" 100.00 1500 100.00 100.00 2.04e-10 REF NP_001089182 "RecQ helicase-like 4 [Xenopus laevis]" 100.00 1503 100.00 100.00 2.25e-10 stop_ save_ ############# # Ligands # ############# save_ZN _Saveframe_category ligand _Mol_type NON-POLYMER _Name_common '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_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RecQ4_zinc_knuckle 'African clawed frog' 8355 Eukaryota Metazoa Xenopus laevis 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 $RecQ4_zinc_knuckle 'chemical synthesis' . . . . . $entity_ZN '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 _Isotopic_labeling $RecQ4_zinc_knuckle 1.1 mM 'natural abundance' $entity_ZN 1.25 mM 'natural abundance' D2O 10 % '[U-100% 2H]' 'sodium phosphate pH 6.3' 20 mM 'natural abundance' 'potassium chloride' 150 mM 'natural abundance' DTT 4 mM 'natural abundance' DSS 0.3 mM 'natural abundance' H2O 90 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.0 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_CcpNMR _Saveframe_category software _Name CcpNMR _Version 2.5.1 loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_ARIA _Saveframe_category software _Name ARIA _Version 2.3.1 loop_ _Vendor _Address _Electronic_address "Linge, O'Donoghue and Nilges" . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_TALOS _Saveframe_category software _Name TALOS _Version . loop_ _Vendor _Address _Electronic_address 'Cornilescu, Delaglio and Bax' . . stop_ loop_ _Task 'dihedral angle calculations' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'geometry optimization' refinement 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_1D_1H_1 _Saveframe_category NMR_applied_experiment _Experiment_name '1D 1H' _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_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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_NOESY_5 _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' 170 . mM pH 6.3 . 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 '2D 1H-15N HSQC' '2D 1H-13C HSQC' '2D 1H-1H TOCSY' '2D 1H-1H 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 RecQ4_zinc_knuckle _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 ASN HA H 4.324 0.004 1 2 1 1 ASN HB2 H 2.946 0.003 1 3 1 1 ASN HB3 H 2.946 0.003 1 4 1 1 ASN HD21 H 6.982 0.001 1 5 1 1 ASN HD22 H 7.663 0.002 1 6 1 1 ASN CA C 52.801 0.313 1 7 1 1 ASN CB C 38.070 0.313 1 8 2 2 ARG H H 8.782 0.002 1 9 2 2 ARG HA H 4.418 0.003 1 10 2 2 ARG HB2 H 1.758 0.003 2 11 2 2 ARG HB3 H 1.867 0.003 2 12 2 2 ARG HG2 H 1.598 0.003 1 13 2 2 ARG HG3 H 1.598 0.003 1 14 2 2 ARG HD2 H 3.117 0.003 1 15 2 2 ARG HD3 H 3.117 0.003 1 16 2 2 ARG HE H 7.208 0.002 1 17 2 2 ARG CA C 56.449 0.313 1 18 2 2 ARG CB C 30.914 0.029 1 19 3 3 SER H H 8.448 0.002 1 20 3 3 SER HA H 4.362 0.002 1 21 3 3 SER HB2 H 3.850 0.002 2 22 3 3 SER HB3 H 3.850 0.002 2 23 3 3 SER CA C 59.152 0.313 1 24 3 3 SER CB C 63.848 0.313 1 25 3 3 SER N N 118.047 0.068 1 26 4 4 GLY H H 8.341 0.003 1 27 4 4 GLY HA2 H 4.009 0.002 2 28 4 4 GLY HA3 H 3.904 0.005 2 29 4 4 GLY CA C 45.309 0.313 1 30 4 4 GLY N N 111.039 0.068 1 31 5 5 ASP H H 8.080 0.001 1 32 5 5 ASP HA H 4.588 0.001 1 33 5 5 ASP HB2 H 2.475 0.004 1 34 5 5 ASP HB3 H 2.475 0.004 1 35 5 5 ASP CA C 54.538 0.313 1 36 5 5 ASP CB C 41.127 0.313 1 37 5 5 ASP N N 121.392 0.068 1 38 6 6 THR H H 7.921 0.002 1 39 6 6 THR HA H 4.461 0.001 1 40 6 6 THR HB H 3.845 0.002 1 41 6 6 THR HG2 H 1.000 0.002 1 42 6 6 THR CA C 60.271 0.313 1 43 6 6 THR CB C 71.123 0.313 1 44 6 6 THR N N 114.919 0.068 1 45 7 7 CYS H H 8.639 0.002 1 46 7 7 CYS HA H 4.273 0.005 1 47 7 7 CYS HB2 H 2.034 0.004 2 48 7 7 CYS HB3 H 2.758 0.002 2 49 7 7 CYS CA C 59.912 0.313 1 50 7 7 CYS CB C 30.038 0.007 1 51 7 7 CYS N N 128.549 0.068 1 52 8 8 PHE H H 8.519 0.004 1 53 8 8 PHE HA H 4.582 0.002 1 54 8 8 PHE HB2 H 3.175 0.002 2 55 8 8 PHE HB3 H 3.343 0.002 2 56 8 8 PHE HD1 H 7.319 0.001 3 57 8 8 PHE HD2 H 7.319 0.001 3 58 8 8 PHE HE1 H 7.394 0.001 3 59 8 8 PHE HE2 H 7.394 0.001 3 60 8 8 PHE HZ H 7.344 0.003 1 61 8 8 PHE CA C 54.745 0.313 1 62 8 8 PHE CB C 38.551 0.313 1 63 8 8 PHE N N 129.290 0.068 1 64 9 9 ARG H H 9.107 0.003 1 65 9 9 ARG HA H 4.219 0.004 1 66 9 9 ARG HB2 H 1.970 0.003 2 67 9 9 ARG HB3 H 1.874 0.003 2 68 9 9 ARG HG2 H 1.422 0.005 2 69 9 9 ARG HG3 H 1.366 0.017 2 70 9 9 ARG HD2 H 3.183 0.004 2 71 9 9 ARG HD3 H 3.182 0.004 2 72 9 9 ARG HE H 7.127 0.002 1 73 9 9 ARG CA C 58.926 0.313 1 74 9 9 ARG CB C 30.936 0.009 1 75 9 9 ARG N N 124.302 0.068 1 76 10 10 CYS H H 8.504 0.004 1 77 10 10 CYS HA H 5.021 0.002 1 78 10 10 CYS HB2 H 3.254 0.002 2 79 10 10 CYS HB3 H 2.585 0.001 2 80 10 10 CYS CA C 58.434 0.313 1 81 10 10 CYS CB C 32.591 0.004 1 82 10 10 CYS N N 117.243 0.068 1 83 11 11 GLY H H 8.205 0.007 1 84 11 11 GLY HA2 H 3.852 0.003 2 85 11 11 GLY HA3 H 4.204 0.002 2 86 11 11 GLY CA C 45.885 0.313 1 87 11 11 GLY N N 115.166 0.068 1 88 12 12 GLY H H 9.198 0.003 1 89 12 12 GLY HA2 H 3.684 0.001 2 90 12 12 GLY HA3 H 4.193 0.004 2 91 12 12 GLY CA C 43.567 0.016 1 92 12 12 GLY N N 113.681 0.068 1 93 13 13 MET H H 8.318 0.003 1 94 13 13 MET HA H 4.345 0.001 1 95 13 13 MET HB2 H 2.028 0.003 2 96 13 13 MET HB3 H 1.899 0.003 2 97 13 13 MET HG2 H 2.513 0.009 2 98 13 13 MET HG3 H 2.542 0.012 2 99 13 13 MET CA C 55.851 0.313 1 100 13 13 MET CB C 34.580 0.007 1 101 13 13 MET N N 117.847 0.068 1 102 14 14 GLY H H 8.601 0.002 1 103 14 14 GLY HA2 H 3.690 0.002 2 104 14 14 GLY HA3 H 4.208 0.002 2 105 14 14 GLY CA C 45.798 0.010 1 106 14 14 GLY N N 108.829 0.068 1 107 15 15 HIS H H 7.052 0.001 1 108 15 15 HIS HA H 4.609 0.002 1 109 15 15 HIS HB2 H 3.116 0.003 2 110 15 15 HIS HB3 H 3.116 0.003 2 111 15 15 HIS HD1 H 12.095 0.004 1 112 15 15 HIS HD2 H 6.902 0.001 1 113 15 15 HIS HE1 H 7.616 0.001 1 114 15 15 HIS CB C 30.190 0.313 1 115 15 15 HIS N N 113.829 0.068 1 116 16 16 TRP H H 8.249 0.002 1 117 16 16 TRP HA H 5.017 0.002 1 118 16 16 TRP HB2 H 3.136 0.002 2 119 16 16 TRP HB3 H 3.544 0.002 2 120 16 16 TRP HD1 H 7.280 0.001 1 121 16 16 TRP HE1 H 10.188 0.002 1 122 16 16 TRP HE3 H 7.667 0.003 1 123 16 16 TRP HZ2 H 7.495 0.002 1 124 16 16 TRP HZ3 H 7.253 0.005 1 125 16 16 TRP HH2 H 7.180 0.004 1 126 16 16 TRP CA C 58.405 0.313 1 127 16 16 TRP CB C 31.082 0.013 1 128 16 16 TRP N N 118.974 0.068 1 129 17 17 ALA H H 9.004 0.001 1 130 17 17 ALA HA H 4.909 0.002 1 131 17 17 ALA HB H 1.420 0.002 1 132 17 17 ALA CB C 19.408 0.313 1 133 17 17 ALA N N 125.898 0.068 1 134 18 18 SER H H 8.049 0.009 1 135 18 18 SER HA H 4.449 0.003 1 136 18 18 SER HB2 H 3.811 0.004 1 137 18 18 SER HB3 H 3.811 0.004 1 138 18 18 SER CA C 58.277 0.313 1 139 18 18 SER CB C 64.054 0.313 1 140 18 18 SER N N 116.139 0.068 1 141 19 19 GLN H H 8.046 0.004 1 142 19 19 GLN HA H 4.544 0.003 1 143 19 19 GLN HB2 H 2.025 0.003 2 144 19 19 GLN HB3 H 2.025 0.003 2 145 19 19 GLN HG2 H 2.341 0.009 2 146 19 19 GLN HG3 H 2.341 0.009 2 147 19 19 GLN HE21 H 7.530 0.001 1 148 19 19 GLN HE22 H 6.758 0.001 1 149 19 19 GLN CA C 54.309 0.313 1 150 19 19 GLN CB C 27.411 0.313 1 151 19 19 GLN N N 121.007 0.068 1 152 20 20 CYS H H 7.476 0.001 1 153 20 20 CYS HA H 4.087 0.003 1 154 20 20 CYS HB2 H 2.815 0.008 2 155 20 20 CYS HB3 H 3.203 0.003 2 156 20 20 CYS CA C 58.721 0.313 1 157 20 20 CYS CB C 30.379 0.047 1 158 20 20 CYS N N 125.766 0.068 1 159 21 21 PRO HA H 4.442 0.004 1 160 21 21 PRO HB2 H 1.960 0.003 2 161 21 21 PRO HB3 H 2.156 0.004 2 162 21 21 PRO HG2 H 1.796 0.004 2 163 21 21 PRO HG3 H 1.864 0.005 2 164 21 21 PRO HD2 H 3.125 0.004 2 165 21 21 PRO HD3 H 3.448 0.001 2 166 21 21 PRO CA C 63.773 0.313 1 167 21 21 PRO CB C 32.158 0.011 1 168 22 22 GLY H H 8.178 0.002 1 169 22 22 GLY HA2 H 4.025 0.005 2 170 22 22 GLY HA3 H 3.963 0.002 2 171 22 22 GLY CA C 45.260 0.024 1 172 22 22 GLY N N 111.939 0.068 1 173 23 23 SER H H 8.747 0.002 1 174 23 23 SER HA H 3.967 0.004 1 175 23 23 SER HB2 H 3.866 0.004 2 176 23 23 SER HB3 H 3.866 0.004 2 177 23 23 SER CA C 62.688 0.313 1 178 23 23 SER CB C 63.710 0.313 1 179 23 23 SER N N 111.818 0.068 1 180 24 24 VAL H H 8.089 0.003 1 181 24 24 VAL HA H 4.456 0.005 1 182 24 24 VAL HB H 2.111 0.004 1 183 24 24 VAL HG1 H 0.925 0.015 2 184 24 24 VAL HG2 H 0.967 0.005 2 185 24 24 VAL CA C 60.035 0.313 1 186 24 24 VAL CB C 32.627 0.313 1 187 24 24 VAL N N 123.284 0.068 1 188 25 25 PRO HA H 4.355 0.004 1 189 25 25 PRO HB2 H 2.301 0.004 2 190 25 25 PRO HB3 H 1.928 0.002 2 191 25 25 PRO HG2 H 2.052 0.005 2 192 25 25 PRO HG3 H 1.977 0.005 2 193 25 25 PRO HD2 H 3.866 0.009 2 194 25 25 PRO HD3 H 3.689 0.004 2 195 25 25 PRO CA C 63.298 0.313 1 196 25 25 PRO CB C 32.360 0.008 1 stop_ save_