data_19505 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; WW Domain Strand-Swapped Dimer ; _BMRB_accession_number 19505 _BMRB_flat_file_name bmr19505.str _Entry_type original _Submission_date 2013-09-18 _Accession_date 2013-09-18 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'A "dumbell" or strand-swapped homodimeric WW domain; essentially a disulfide/beta-sheet hub with entire WW domains as end-caps. Designed using a stand-alone version of Foldit.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kier Brandon L. . 2 Sheffler William . . 3 Baker David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 182 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-09-29 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 19503 'WW Domain with Loop 1 Excised' 19504 baa38 stop_ _Original_release_date 2014-09-29 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Covalent Assembly of Homooligomeric Proteins Using Structure-templating Hubs' _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 Kier Brandon L. . 2 Sheffler William . . 3 Baker David . . stop_ _Journal_abbreviation Biochemistry _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 'WW Domain Strand-Swapped Dimer' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'WW Domain Strand-Swapped Dimer 1' $entity 'WW Domain Strand-Swapped Dimer 2' $entity 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 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 3363.901 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; KLPPGWEKRCFYFNRITGKR QFERPSD ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 LEU 3 PRO 4 PRO 5 GLY 6 TRP 7 GLU 8 LYS 9 ARG 10 CYS 11 PHE 12 TYR 13 PHE 14 ASN 15 ARG 16 ILE 17 THR 18 GLY 19 LYS 20 ARG 21 GLN 22 PHE 23 GLU 24 ARG 25 PRO 26 SER 27 ASP 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 . . . . . . 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 _Details $entity 'chemical synthesis' . . . . . 'Synthesized by GenScript, but dimerization and purification performed in-house. (University of Washington)' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM protein (0.5 mM dimer)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity . mM 'natural abundance' 'sodium phosphate' 50 mM 'natural abundance' DSS 0.5 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_Foldit _Saveframe_category software _Name Foldit _Version . loop_ _Vendor _Address _Electronic_address 'David Baker et al, University of Washington' . . stop_ loop_ _Task design stop_ _Details 'Stand-alone version of Foldit used to design & optimize the initial structure and model NOEs for refinement.' save_ save_CNS _Saveframe_category software _Name CNS _Version 1.2 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _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_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . 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' 0.11 . M pH 6.5 . pH pressure 1 . atm temperature 280 . 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 H 1 'methyl protons' ppm 0.00 internal direct . . . 1 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 TOCSY' 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 'WW Domain Strand-Swapped Dimer 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 LYS HA H 4.170 0.01 1 2 1 1 LYS HB2 H 2.022 0.01 2 3 1 1 LYS HB3 H 2.022 0.01 2 4 1 1 LYS HG2 H 1.585 0.01 2 5 1 1 LYS HG3 H 1.585 0.01 2 6 1 1 LYS HD2 H 1.813 0.01 2 7 1 1 LYS HD3 H 1.813 0.01 2 8 2 2 LEU H H 8.972 0.02 1 9 2 2 LEU HA H 4.718 0.01 1 10 2 2 LEU HB2 H 1.895 0.01 2 11 2 2 LEU HB3 H 1.521 0.01 2 12 2 2 LEU HG H 1.967 0.01 1 13 2 2 LEU HD1 H 1.133 0.01 1 14 2 2 LEU HD2 H 0.896 0.01 1 15 3 3 PRO HA H 4.942 0.01 1 16 3 3 PRO HB2 H 2.081 0.01 1 17 3 3 PRO HB3 H 2.739 0.01 1 18 3 3 PRO HG2 H 1.740 0.01 1 19 3 3 PRO HG3 H 1.891 0.01 1 20 3 3 PRO HD2 H 3.118 0.01 1 21 3 3 PRO HD3 H 3.808 0.01 1 22 4 4 PRO HA H 4.458 0.01 1 23 4 4 PRO HB2 H 1.990 0.01 1 24 4 4 PRO HB3 H 2.437 0.01 1 25 4 4 PRO HG2 H 2.162 0.01 1 26 4 4 PRO HG3 H 2.263 0.01 1 27 4 4 PRO HD2 H 3.749 0.01 1 28 4 4 PRO HD3 H 4.028 0.01 1 29 5 5 GLY H H 8.946 0.02 1 30 5 5 GLY HA2 H 4.228 0.01 1 31 5 5 GLY HA3 H 3.583 0.01 1 32 6 6 TRP H H 7.628 0.02 1 33 6 6 TRP HA H 5.260 0.01 1 34 6 6 TRP HB2 H 3.365 0.01 1 35 6 6 TRP HB3 H 3.041 0.01 1 36 6 6 TRP HD1 H 7.074 0.01 1 37 6 6 TRP HE1 H 10.84 0.01 1 38 6 6 TRP HE3 H 7.507 0.01 1 39 6 6 TRP HZ2 H 7.614 0.01 1 40 6 6 TRP HZ3 H 7.047 0.01 1 41 6 6 TRP HH2 H 6.910 0.01 1 42 7 7 GLU H H 9.730 0.02 1 43 7 7 GLU HA H 4.919 0.01 1 44 7 7 GLU HB2 H 2.235 0.01 2 45 7 7 GLU HB3 H 2.114 0.01 2 46 7 7 GLU HG2 H 2.688 0.01 2 47 7 7 GLU HG3 H 2.383 0.01 2 48 8 8 LYS H H 9.146 0.02 1 49 8 8 LYS HA H 4.564 0.01 1 50 8 8 LYS HB2 H 1.895 0.01 2 51 8 8 LYS HB3 H 1.666 0.01 2 52 8 8 LYS HG2 H 0.940 0.01 2 53 8 8 LYS HG3 H 0.940 0.01 2 54 9 9 ARG H H 8.859 0.02 1 55 9 9 ARG HA H 4.660 0.01 1 56 9 9 ARG HB2 H 1.502 0.01 1 57 9 9 ARG HB3 H 0.422 0.01 1 58 9 9 ARG HG2 H 1.434 0.01 2 59 9 9 ARG HG3 H 1.434 0.01 2 60 9 9 ARG HD2 H 3.068 0.01 2 61 9 9 ARG HD3 H 2.929 0.01 2 62 9 9 ARG HE H 7.253 0.01 1 63 9 9 ARG HH11 H 6.401 0.04 2 64 9 9 ARG HH12 H 6.401 0.04 2 65 10 10 CYS H H 8.591 0.02 1 66 10 10 CYS HA H 5.550 0.01 1 67 10 10 CYS HB2 H 2.828 0.01 1 68 10 10 CYS HB3 H 2.771 0.01 1 69 11 11 PHE H H 8.846 0.02 1 70 11 11 PHE HA H 4.986 0.01 1 71 11 11 PHE HB2 H 3.114 0.01 2 72 11 11 PHE HB3 H 2.926 0.01 2 73 11 11 PHE HD1 H 7.222 0.01 3 74 11 11 PHE HD2 H 7.222 0.01 3 75 11 11 PHE HE1 H 7.252 0.01 3 76 11 11 PHE HE2 H 7.252 0.01 3 77 11 11 PHE HZ H 7.340 0.01 1 78 12 12 TYR H H 9.388 0.02 1 79 12 12 TYR HA H 5.493 0.01 1 80 12 12 TYR HB2 H 3.098 0.01 1 81 12 12 TYR HB3 H 2.812 0.01 1 82 12 12 TYR HD1 H 6.921 0.01 3 83 12 12 TYR HD2 H 6.921 0.01 3 84 12 12 TYR HE1 H 6.847 0.01 3 85 12 12 TYR HE2 H 6.847 0.01 3 86 13 13 PHE H H 9.655 0.02 1 87 13 13 PHE HA H 5.858 0.01 1 88 13 13 PHE HB2 H 3.114 0.01 2 89 13 13 PHE HB3 H 2.814 0.01 2 90 13 13 PHE HD1 H 7.081 0.01 3 91 13 13 PHE HD2 H 7.081 0.01 3 92 13 13 PHE HE1 H 7.261 0.01 3 93 13 13 PHE HE2 H 7.261 0.01 3 94 13 13 PHE HZ H 7.373 0.01 1 95 14 14 ASN H H 8.431 0.02 1 96 14 14 ASN HA H 4.300 0.01 1 97 14 14 ASN HB2 H 2.171 0.01 1 98 14 14 ASN HB3 H -0.52 0.01 1 99 14 14 ASN HD21 H 4.287 0.01 1 100 14 14 ASN HD22 H 6.760 0.01 1 101 15 15 ARG H H 8.375 0.02 1 102 15 15 ARG HA H 3.870 0.01 1 103 15 15 ARG HB2 H 1.904 0.01 2 104 15 15 ARG HB3 H 1.799 0.01 2 105 15 15 ARG HG2 H 1.756 0.01 2 106 15 15 ARG HG3 H 1.603 0.01 2 107 15 15 ARG HD2 H 3.317 0.01 2 108 15 15 ARG HD3 H 3.264 0.01 2 109 15 15 ARG HE H 7.499 0.01 1 110 16 16 ILE H H 8.284 0.02 1 111 16 16 ILE HA H 3.890 0.01 1 112 16 16 ILE HB H 2.124 0.01 1 113 16 16 ILE HG12 H 1.526 0.01 1 114 16 16 ILE HG13 H 1.156 0.01 1 115 16 16 ILE HG2 H 0.874 0.01 1 116 16 16 ILE HD1 H 0.837 0.01 1 117 17 17 THR H H 7.680 0.02 1 118 17 17 THR HA H 4.245 0.01 1 119 17 17 THR HB H 4.320 0.01 1 120 17 17 THR HG1 H 5.434 0.04 1 121 17 17 THR HG2 H 1.104 0.01 1 122 18 18 GLY H H 8.291 0.02 1 123 18 18 GLY HA2 H 4.147 0.01 1 124 18 18 GLY HA3 H 3.671 0.01 1 125 19 19 LYS H H 7.176 0.02 1 126 19 19 LYS HA H 4.315 0.01 1 127 19 19 LYS HB2 H 1.847 0.01 2 128 19 19 LYS HB3 H 1.624 0.01 2 129 19 19 LYS HG2 H 1.533 0.01 2 130 19 19 LYS HG3 H 1.524 0.01 2 131 19 19 LYS HE2 H 3.172 0.01 2 132 19 19 LYS HE3 H 3.172 0.01 2 133 20 20 ARG H H 8.614 0.02 1 134 20 20 ARG HA H 6.088 0.01 1 135 20 20 ARG HB2 H 1.933 0.01 2 136 20 20 ARG HB3 H 1.846 0.01 2 137 21 21 GLN H H 9.523 0.02 1 138 21 21 GLN HA H 5.026 0.01 1 139 21 21 GLN HB2 H 2.621 0.01 1 140 21 21 GLN HB3 H 2.311 0.01 1 141 21 21 GLN HG2 H 2.624 0.01 1 142 21 21 GLN HG3 H 2.304 0.01 1 143 21 21 GLN HE21 H 7.405 0.01 1 144 21 21 GLN HE22 H 6.889 0.01 1 145 22 22 PHE H H 9.243 0.02 1 146 22 22 PHE HA H 4.929 0.01 1 147 22 22 PHE HB2 H 3.528 0.01 2 148 22 22 PHE HB3 H 3.131 0.01 2 149 22 22 PHE HD1 H 7.690 0.01 3 150 22 22 PHE HD2 H 7.690 0.01 3 151 22 22 PHE HE1 H 7.338 0.01 3 152 22 22 PHE HE2 H 7.338 0.01 3 153 22 22 PHE HZ H 7.251 0.01 1 154 23 23 GLU H H 8.326 0.02 1 155 23 23 GLU HA H 4.502 0.01 1 156 23 23 GLU HB2 H 2.019 0.01 2 157 23 23 GLU HB3 H 2.019 0.01 2 158 23 23 GLU HG2 H 2.516 0.01 2 159 23 23 GLU HG3 H 2.516 0.01 2 160 24 24 ARG H H 8.743 0.02 1 161 24 24 ARG HA H 2.809 0.01 1 162 24 24 ARG HB3 H 1.495 0.01 1 163 24 24 ARG HG2 H 1.315 0.01 2 164 24 24 ARG HG3 H 1.057 0.01 2 165 24 24 ARG HD2 H 3.119 0.01 2 166 24 24 ARG HD3 H 3.119 0.01 2 167 24 24 ARG HE H 7.344 0.01 1 168 25 25 PRO HA H 4.013 0.01 1 169 25 25 PRO HB2 H 0.929 0.01 1 170 25 25 PRO HB3 H 0.800 0.01 1 171 25 25 PRO HG2 H 0.662 0.01 1 172 25 25 PRO HG3 H 0.044 0.01 1 173 25 25 PRO HD2 H 2.337 0.01 1 174 25 25 PRO HD3 H 2.520 0.01 1 175 26 26 SER H H 8.389 0.02 1 176 26 26 SER HA H 4.404 0.01 1 177 26 26 SER HB2 H 3.858 0.01 2 178 26 26 SER HB3 H 3.803 0.01 2 179 27 27 ASP H H 8.261 0.02 1 180 27 27 ASP HA H 4.532 0.01 1 181 27 27 ASP HB2 H 2.905 0.01 2 182 27 27 ASP HB3 H 2.905 0.01 2 stop_ save_