data_19504 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; baa38 ; _BMRB_accession_number 19504 _BMRB_flat_file_name bmr19504.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 beta-alpha-alpha dimer motif held together by a ...WXCXW... hub, and employing the key features of the RHH1 superfamily. Designed & optimized using 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" 248 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' 19505 'WW Domain Strand-Swapped Dimer' 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 baa38 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label baa38_1 $entity baa38_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 4599.372 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 38 _Mol_residue_sequence ; RWLCIWLSDQTLEDLEKMAR REGLSKSEMINVALQHYK ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 TRP 3 LEU 4 CYS 5 ILE 6 TRP 7 LEU 8 SER 9 ASP 10 GLN 11 THR 12 LEU 13 GLU 14 ASP 15 LEU 16 GLU 17 LYS 18 MET 19 ALA 20 ARG 21 ARG 22 GLU 23 GLY 24 LEU 25 SER 26 LYS 27 SER 28 GLU 29 MET 30 ILE 31 ASN 32 VAL 33 ALA 34 LEU 35 GLN 36 HIS 37 TYR 38 LYS 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' . . . . . 'peptide synthesis via GenScript; dimerized and purified 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' H20 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 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 baa38_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 ARG HA H 3.341 0.01 1 2 1 1 ARG HB2 H 1.604 0.01 2 3 1 1 ARG HB3 H 1.562 0.01 2 4 1 1 ARG HG2 H 1.509 0.01 2 5 1 1 ARG HG3 H 1.509 0.01 2 6 1 1 ARG HD2 H 3.095 0.01 2 7 1 1 ARG HD3 H 3.095 0.01 2 8 1 1 ARG HE H 7.234 0.01 1 9 2 2 TRP H H 9.010 0.02 1 10 2 2 TRP HA H 5.088 0.01 1 11 2 2 TRP HB2 H 3.111 0.01 1 12 2 2 TRP HB3 H 3.099 0.01 1 13 2 2 TRP HD1 H 7.459 0.01 1 14 2 2 TRP HE1 H 10.37 0.01 1 15 2 2 TRP HE3 H 7.235 0.01 1 16 2 2 TRP HZ2 H 7.375 0.01 1 17 2 2 TRP HZ3 H 7.076 0.01 1 18 2 2 TRP HH2 H 7.216 0.01 1 19 3 3 LEU H H 9.506 0.02 1 20 3 3 LEU HA H 4.690 0.01 1 21 3 3 LEU HB2 H 1.697 0.01 2 22 3 3 LEU HB3 H 1.261 0.01 2 23 3 3 LEU HG H 1.410 0.01 1 24 3 3 LEU HD1 H 0.856 0.01 1 25 3 3 LEU HD2 H 0.646 0.01 1 26 4 4 CYS H H 8.997 0.02 1 27 4 4 CYS HA H 5.805 0.01 1 28 4 4 CYS HB2 H 2.989 0.01 1 29 4 4 CYS HB3 H 2.636 0.01 1 30 5 5 ILE H H 9.319 0.02 1 31 5 5 ILE HA H 4.775 0.01 1 32 5 5 ILE HB H 1.906 0.01 1 33 5 5 ILE HG12 H 1.444 0.01 2 34 5 5 ILE HG13 H 1.221 0.01 1 35 5 5 ILE HG2 H 0.828 0.01 1 36 5 5 ILE HD1 H 0.760 0.01 1 37 6 6 TRP H H 8.606 0.02 1 38 6 6 TRP HA H 4.356 0.01 1 39 6 6 TRP HB2 H 2.689 0.01 1 40 6 6 TRP HB3 H 1.740 0.01 1 41 6 6 TRP HD1 H 6.669 0.01 1 42 6 6 TRP HE1 H 10.16 0.01 1 43 6 6 TRP HE3 H 5.602 0.01 1 44 6 6 TRP HZ2 H 7.370 0.01 1 45 6 6 TRP HZ3 H 6.734 0.01 1 46 6 6 TRP HH2 H 7.116 0.01 1 47 7 7 LEU H H 7.784 0.02 1 48 7 7 LEU HA H 4.528 0.01 1 49 7 7 LEU HB2 H 1.210 0.01 1 50 7 7 LEU HB3 H 1.157 0.01 1 51 7 7 LEU HG H 1.428 0.01 1 52 7 7 LEU HD1 H 0.802 0.01 2 53 7 7 LEU HD2 H 0.802 0.01 2 54 8 8 SER H H 8.678 0.02 1 55 8 8 SER HA H 4.275 0.01 1 56 8 8 SER HB2 H 4.021 0.01 2 57 8 8 SER HB3 H 4.010 0.01 2 58 9 9 ASP H H 9.066 0.02 1 59 9 9 ASP HA H 4.175 0.01 1 60 9 9 ASP HB2 H 2.782 0.01 2 61 9 9 ASP HB3 H 2.779 0.01 2 62 10 10 GLN H H 8.689 0.02 1 63 10 10 GLN HA H 3.958 0.01 1 64 10 10 GLN HB2 H 2.080 0.01 2 65 10 10 GLN HB3 H 1.898 0.01 2 66 10 10 GLN HG2 H 2.321 0.01 2 67 10 10 GLN HG3 H 2.321 0.01 2 68 10 10 GLN HE21 H 6.994 0.01 1 69 10 10 GLN HE22 H 7.495 0.01 1 70 11 11 THR H H 8.000 0.02 1 71 11 11 THR HA H 4.045 0.01 1 72 11 11 THR HB H 3.852 0.01 1 73 11 11 THR HG2 H 1.207 0.01 1 74 12 12 LEU H H 8.482 0.02 1 75 12 12 LEU HA H 3.832 0.01 1 76 12 12 LEU HB2 H 1.436 0.01 2 77 12 12 LEU HB3 H 1.408 0.01 2 78 12 12 LEU HG H 1.671 0.01 1 79 12 12 LEU HD1 H 0.740 0.01 1 80 12 12 LEU HD2 H 0.617 0.01 1 81 13 13 GLU H H 8.242 0.02 1 82 13 13 GLU HA H 4.031 0.01 1 83 13 13 GLU HB2 H 2.149 0.01 2 84 13 13 GLU HB3 H 2.067 0.01 2 85 13 13 GLU HG2 H 2.527 0.01 2 86 13 13 GLU HG3 H 2.459 0.01 2 87 14 14 ASP H H 8.128 0.02 1 88 14 14 ASP HA H 4.384 0.01 1 89 14 14 ASP HB2 H 3.101 0.01 2 90 14 14 ASP HB3 H 2.917 0.01 2 91 15 15 LEU H H 8.721 0.02 1 92 15 15 LEU HA H 4.018 0.01 1 93 15 15 LEU HB2 H 1.443 0.01 2 94 15 15 LEU HB3 H 1.401 0.01 2 95 15 15 LEU HG H 1.401 0.01 1 96 15 15 LEU HD1 H 0.923 0.01 1 97 15 15 LEU HD2 H 0.737 0.01 1 98 16 16 GLU H H 8.468 0.02 1 99 16 16 GLU HA H 3.919 0.01 1 100 16 16 GLU HB2 H 2.239 0.01 2 101 16 16 GLU HB3 H 2.058 0.01 2 102 16 16 GLU HG2 H 2.554 0.01 2 103 16 16 GLU HG3 H 2.455 0.01 2 104 17 17 LYS H H 8.128 0.02 1 105 17 17 LYS HA H 3.988 0.01 1 106 17 17 LYS HB2 H 1.969 0.01 2 107 17 17 LYS HB3 H 1.898 0.01 2 108 17 17 LYS HG2 H 1.681 0.01 2 109 17 17 LYS HG3 H 1.398 0.01 2 110 17 17 LYS HD2 H 1.686 0.01 2 111 17 17 LYS HD3 H 1.686 0.01 2 112 17 17 LYS HE2 H 2.956 0.01 2 113 17 17 LYS HE3 H 2.956 0.01 2 114 18 18 MET H H 8.403 0.02 1 115 18 18 MET HA H 4.115 0.01 1 116 18 18 MET HB2 H 2.290 0.01 2 117 18 18 MET HB3 H 2.178 0.01 2 118 18 18 MET HG2 H 2.732 0.01 2 119 18 18 MET HG3 H 2.717 0.01 2 120 18 18 MET HE H 2.097 0.01 1 121 19 19 ALA H H 8.719 0.02 1 122 19 19 ALA HA H 3.783 0.01 1 123 19 19 ALA HB H 1.318 0.01 1 124 20 20 ARG H H 7.889 0.02 1 125 20 20 ARG HA H 4.121 0.01 1 126 20 20 ARG HB2 H 1.959 0.01 2 127 20 20 ARG HB3 H 1.898 0.01 2 128 20 20 ARG HG2 H 1.758 0.01 2 129 20 20 ARG HG3 H 1.649 0.01 2 130 20 20 ARG HD2 H 3.210 0.01 2 131 20 20 ARG HD3 H 3.210 0.01 2 132 20 20 ARG HE H 7.244 0.01 1 133 21 21 ARG H H 7.968 0.02 1 134 21 21 ARG HA H 4.080 0.01 1 135 21 21 ARG HB2 H 2.030 0.01 2 136 21 21 ARG HB3 H 2.030 0.01 2 137 21 21 ARG HG2 H 1.742 0.01 2 138 21 21 ARG HG3 H 1.685 0.01 2 139 21 21 ARG HD2 H 3.222 0.01 2 140 21 21 ARG HD3 H 3.222 0.01 2 141 21 21 ARG HE H 7.305 0.01 1 142 22 22 GLU H H 8.035 0.02 1 143 22 22 GLU HA H 4.389 0.01 1 144 22 22 GLU HB2 H 2.325 0.01 2 145 22 22 GLU HB3 H 1.834 0.01 2 146 22 22 GLU HG2 H 2.612 0.01 2 147 22 22 GLU HG3 H 2.487 0.01 2 148 23 23 GLY H H 7.912 0.02 1 149 23 23 GLY HA2 H 3.943 0.01 1 150 23 23 GLY HA3 H 3.916 0.01 1 151 24 24 LEU H H 8.149 0.02 1 152 24 24 LEU HA H 4.840 0.01 1 153 24 24 LEU HB2 H 1.508 0.01 2 154 24 24 LEU HB3 H 1.441 0.01 2 155 24 24 LEU HG H 1.693 0.01 1 156 24 24 LEU HD1 H 0.871 0.01 1 157 24 24 LEU HD2 H 0.826 0.01 1 158 25 25 SER H H 8.182 0.02 1 159 25 25 SER HA H 4.563 0.01 1 160 25 25 SER HB2 H 4.463 0.01 2 161 25 25 SER HB3 H 4.011 0.01 2 162 26 26 LYS H H 9.270 0.02 1 163 26 26 LYS HA H 3.697 0.01 1 164 26 26 LYS HB2 H 2.014 0.01 2 165 26 26 LYS HB3 H 1.827 0.01 2 166 26 26 LYS HG2 H 1.469 0.01 2 167 26 26 LYS HG3 H 1.154 0.01 2 168 26 26 LYS HD2 H 1.824 0.01 1 169 26 26 LYS HD3 H 1.522 0.01 1 170 26 26 LYS HE2 H 3.069 0.01 2 171 26 26 LYS HE3 H 3.027 0.01 2 172 27 27 SER H H 8.615 0.02 1 173 27 27 SER HA H 3.972 0.01 1 174 27 27 SER HB2 H 4.142 0.01 2 175 27 27 SER HB3 H 4.039 0.01 2 176 28 28 GLU H H 7.969 0.02 1 177 28 28 GLU HA H 4.169 0.01 1 178 28 28 GLU HB2 H 2.294 0.01 2 179 28 28 GLU HB3 H 2.090 0.01 2 180 28 28 GLU HG2 H 2.629 0.01 2 181 28 28 GLU HG3 H 2.518 0.01 2 182 29 29 MET H H 8.768 0.02 1 183 29 29 MET HA H 4.239 0.01 1 184 29 29 MET HB2 H 1.831 0.01 2 185 29 29 MET HB3 H 1.716 0.01 2 186 29 29 MET HG2 H 2.648 0.01 2 187 29 29 MET HG3 H 2.294 0.01 2 188 29 29 MET HE H 1.722 0.01 1 189 30 30 ILE H H 7.966 0.02 1 190 30 30 ILE HA H 3.375 0.01 1 191 30 30 ILE HB H 1.915 0.01 1 192 30 30 ILE HG12 H 0.921 0.01 1 193 30 30 ILE HG13 H 0.921 0.01 1 194 30 30 ILE HG2 H 0.756 0.01 1 195 30 30 ILE HD1 H 0.762 0.01 1 196 31 31 ASN H H 7.862 0.02 1 197 31 31 ASN HA H 4.236 0.01 1 198 31 31 ASN HB2 H 2.931 0.01 2 199 31 31 ASN HB3 H 2.877 0.01 2 200 31 31 ASN HD21 H 7.093 0.01 1 201 31 31 ASN HD22 H 7.572 0.01 1 202 32 32 VAL H H 8.463 0.02 1 203 32 32 VAL HA H 3.708 0.01 1 204 32 32 VAL HB H 1.990 0.01 1 205 32 32 VAL HG1 H 1.025 0.01 1 206 32 32 VAL HG2 H 0.756 0.01 1 207 33 33 ALA H H 8.285 0.02 1 208 33 33 ALA HA H 3.815 0.01 1 209 33 33 ALA HB H 1.167 0.01 1 210 34 34 LEU H H 8.506 0.02 1 211 34 34 LEU HA H 3.952 0.01 1 212 34 34 LEU HB2 H 2.058 0.01 2 213 34 34 LEU HB3 H 1.822 0.01 2 214 34 34 LEU HG H 1.351 0.01 1 215 34 34 LEU HD1 H 0.735 0.01 1 216 34 34 LEU HD2 H 0.677 0.01 1 217 35 35 GLN H H 8.340 0.02 1 218 35 35 GLN HA H 3.999 0.01 1 219 35 35 GLN HB2 H 2.108 0.01 2 220 35 35 GLN HB3 H 2.006 0.01 2 221 35 35 GLN HG2 H 2.552 0.01 2 222 35 35 GLN HG3 H 2.330 0.01 2 223 35 35 GLN HE21 H 6.787 0.01 1 224 35 35 GLN HE22 H 7.375 0.01 1 225 36 36 HIS H H 7.859 0.02 1 226 36 36 HIS HA H 4.525 0.01 1 227 36 36 HIS HB2 H 3.653 0.01 2 228 36 36 HIS HB3 H 3.182 0.01 2 229 36 36 HIS HD2 H 7.577 0.01 1 230 36 36 HIS HE1 H 8.696 0.01 1 231 37 37 TYR H H 7.655 0.02 1 232 37 37 TYR HA H 4.298 0.01 1 233 37 37 TYR HB2 H 3.241 0.01 1 234 37 37 TYR HB3 H 2.982 0.01 1 235 37 37 TYR HD1 H 6.987 0.01 3 236 37 37 TYR HD2 H 6.987 0.01 3 237 37 37 TYR HE1 H 6.389 0.01 3 238 37 37 TYR HE2 H 6.389 0.01 3 239 38 38 LYS H H 7.938 0.02 1 240 38 38 LYS HA H 4.046 0.01 1 241 38 38 LYS HB2 H 1.728 0.01 2 242 38 38 LYS HB3 H 1.594 0.01 2 243 38 38 LYS HG2 H 1.346 0.01 2 244 38 38 LYS HG3 H 1.291 0.01 2 245 38 38 LYS HD2 H 1.572 0.01 2 246 38 38 LYS HD3 H 1.572 0.01 2 247 38 38 LYS HE2 H 2.906 0.01 2 248 38 38 LYS HE3 H 2.906 0.01 2 stop_ save_