data_19503 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Circular Permutant of the WW Domain with Loop 1 Excised ; _BMRB_accession_number 19503 _BMRB_flat_file_name bmr19503.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 ; This miniprotein construct represents a circular permutation of the Pin1 WW domain (loop 1 excision), with some additional mutations for stability and removal of chromophore redundancy. The structure is very similar to that of wild-type WW Pin1, except of course for the termini and loop 1. This miniprotein was not designed with native-like ligand-binding function in mind. ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kier Brandon L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 211 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-01-31 update BMRB 'update entry citation' 2014-01-13 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 19504 baa38 19505 'WW Domain Strand-Swapped Dimer' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Circular Permutation of a WW Domain: Folding Still Occurs after Excising the Turn of the Folding-Nucleating Hairpin.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24350581 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kier Brandon L. . 2 Anderson Jordan M. . 3 Andersen Niels H. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemical Society' _Journal_volume 136 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 741 _Page_last 749 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'WW Domain with Loop 1 Excised' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'WW Domain with Loop 1 Excised' $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 3794.438 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; RWFYFNRITGKRQFERPKGL VKGWEKRWD ; loop_ _Residue_seq_code _Residue_label 1 ARG 2 TRP 3 PHE 4 TYR 5 PHE 6 ASN 7 ARG 8 ILE 9 THR 10 GLY 11 LYS 12 ARG 13 GLN 14 PHE 15 GLU 16 ARG 17 PRO 18 LYS 19 GLY 20 LEU 21 VAL 22 LYS 23 GLY 24 TRP 25 GLU 26 LYS 27 ARG 28 TRP 29 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-09 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 2MDU "Circular Permutant Of The Ww Domain With Loop 1 Excised" 100.00 29 100.00 100.00 4.51e-11 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 . . . . . . 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' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '50 mM phosphate buffer, pH 6.5, with DSS standard' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1.2 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_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 . . . 1.000000000 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 with Loop 1 Excised' _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 3.572 0.01 1 2 1 1 ARG HB2 H 1.860 0.01 1 3 1 1 ARG HB3 H 1.860 0.01 1 4 1 1 ARG HG2 H 1.745 0.01 2 5 1 1 ARG HG3 H 1.610 0.01 2 6 1 1 ARG HE H 7.403 0.01 1 7 2 2 TRP H H 8.666 0.02 1 8 2 2 TRP HA H 5.561 0.01 1 9 2 2 TRP HB2 H 3.154 0.01 1 10 2 2 TRP HB3 H 2.859 0.01 1 11 2 2 TRP HD1 H 7.535 0.01 1 12 2 2 TRP HE1 H 10.44 0.01 1 13 2 2 TRP HE3 H 7.640 0.01 1 14 2 2 TRP HZ2 H 7.420 0.01 1 15 2 2 TRP HZ3 H 7.042 0.01 1 16 2 2 TRP HH2 H 7.181 0.01 1 17 3 3 PHE H H 9.545 0.02 1 18 3 3 PHE HA H 4.970 0.01 1 19 3 3 PHE HB2 H 3.047 0.01 1 20 3 3 PHE HB3 H 2.727 0.01 1 21 3 3 PHE HD1 H 7.055 0.01 3 22 3 3 PHE HD2 H 7.055 0.01 3 23 3 3 PHE HE1 H 7.002 0.01 3 24 3 3 PHE HE2 H 7.002 0.01 3 25 3 3 PHE HZ H 7.104 0.01 1 26 4 4 TYR H H 9.247 0.02 1 27 4 4 TYR HA H 5.351 0.01 1 28 4 4 TYR HB2 H 2.943 0.01 1 29 4 4 TYR HB3 H 2.677 0.01 1 30 4 4 TYR HD1 H 6.844 0.01 3 31 4 4 TYR HD2 H 6.844 0.01 3 32 4 4 TYR HE1 H 6.743 0.01 3 33 4 4 TYR HE2 H 6.743 0.01 3 34 5 5 PHE H H 9.728 0.02 1 35 5 5 PHE HA H 5.669 0.01 1 36 5 5 PHE HB2 H 3.069 0.01 1 37 5 5 PHE HB3 H 2.777 0.01 1 38 5 5 PHE HD1 H 7.005 0.01 3 39 5 5 PHE HD2 H 7.005 0.01 3 40 5 5 PHE HE1 H 7.219 0.01 3 41 5 5 PHE HE2 H 7.219 0.01 3 42 5 5 PHE HZ H 7.316 0.01 1 43 6 6 ASN H H 8.374 0.02 1 44 6 6 ASN HA H 4.326 0.01 1 45 6 6 ASN HB2 H 2.132 0.01 1 46 6 6 ASN HB3 H -0.51 0.01 1 47 6 6 ASN HD21 H 3.771 0.01 1 48 6 6 ASN HD22 H 6.583 0.01 1 49 7 7 ARG H H 8.391 0.02 1 50 7 7 ARG HA H 3.846 0.01 1 51 7 7 ARG HB2 H 1.819 0.01 1 52 7 7 ARG HB3 H 1.822 0.01 1 53 7 7 ARG HG2 H 1.725 0.01 2 54 7 7 ARG HG3 H 1.620 0.01 2 55 7 7 ARG HD2 H 3.337 0.01 2 56 7 7 ARG HD3 H 3.203 0.01 2 57 7 7 ARG HE H 7.602 0.01 1 58 8 8 ILE H H 8.067 0.02 1 59 8 8 ILE HA H 3.835 0.01 1 60 8 8 ILE HB H 2.013 0.01 1 61 8 8 ILE HG12 H 1.466 0.01 2 62 8 8 ILE HG13 H 1.079 0.01 2 63 8 8 ILE HG2 H 0.796 0.01 1 64 8 8 ILE HD1 H 0.766 0.01 1 65 9 9 THR H H 7.709 0.02 1 66 9 9 THR HA H 4.174 0.01 1 67 9 9 THR HB H 4.223 0.01 1 68 9 9 THR HG2 H 1.013 0.01 1 69 10 10 GLY H H 8.311 0.02 1 70 10 10 GLY HA2 H 4.023 0.01 1 71 10 10 GLY HA3 H 3.535 0.01 1 72 11 11 LYS H H 7.005 0.02 1 73 11 11 LYS HA H 4.294 0.01 1 74 11 11 LYS HB2 H 1.848 0.01 2 75 11 11 LYS HB3 H 1.523 0.01 2 76 11 11 LYS HG2 H 1.448 0.01 2 77 11 11 LYS HG3 H 1.393 0.01 2 78 11 11 LYS HD2 H 1.742 0.01 2 79 11 11 LYS HD3 H 1.742 0.01 2 80 11 11 LYS HE2 H 3.056 0.01 2 81 11 11 LYS HE3 H 3.056 0.01 2 82 12 12 ARG H H 8.517 0.02 1 83 12 12 ARG HA H 6.152 0.01 1 84 12 12 ARG HB2 H 1.970 0.01 1 85 12 12 ARG HB3 H 1.856 0.01 1 86 12 12 ARG HG2 H 1.802 0.01 2 87 12 12 ARG HG3 H 1.608 0.01 2 88 12 12 ARG HD2 H 2.876 0.01 2 89 12 12 ARG HD3 H 2.856 0.01 2 90 12 12 ARG HE H 6.651 0.01 1 91 13 13 GLN H H 9.431 0.02 1 92 13 13 GLN HA H 4.842 0.01 1 93 13 13 GLN HB2 H 2.147 0.01 1 94 13 13 GLN HB3 H 2.116 0.01 1 95 13 13 GLN HG2 H 2.486 0.01 1 96 13 13 GLN HG3 H 2.421 0.01 1 97 13 13 GLN HE21 H 7.256 0.01 2 98 13 13 GLN HE22 H 6.550 0.01 2 99 14 14 PHE H H 9.110 0.02 1 100 14 14 PHE HA H 4.911 0.01 1 101 14 14 PHE HB2 H 3.446 0.01 2 102 14 14 PHE HB3 H 2.991 0.01 2 103 14 14 PHE HD1 H 7.583 0.01 3 104 14 14 PHE HD2 H 7.583 0.01 3 105 14 14 PHE HE1 H 7.274 0.01 3 106 14 14 PHE HE2 H 7.274 0.01 3 107 14 14 PHE HZ H 7.191 0.01 1 108 15 15 GLU H H 8.138 0.02 1 109 15 15 GLU HA H 4.371 0.01 1 110 15 15 GLU HB2 H 1.881 0.01 1 111 15 15 GLU HB3 H 1.869 0.01 1 112 15 15 GLU HG2 H 2.297 0.01 1 113 15 15 GLU HG3 H 2.257 0.01 1 114 16 16 ARG H H 8.549 0.02 1 115 16 16 ARG HA H 2.901 0.01 1 116 16 16 ARG HB2 H 1.429 0.01 1 117 16 16 ARG HB3 H 1.408 0.01 1 118 16 16 ARG HG2 H 1.128 0.01 2 119 16 16 ARG HG3 H 1.128 0.01 2 120 17 17 PRO HA H 3.787 0.01 1 121 17 17 PRO HB2 H 1.076 0.01 1 122 17 17 PRO HB3 H 0.988 0.01 1 123 17 17 PRO HG2 H 0.551 0.01 1 124 17 17 PRO HG3 H 0.012 0.01 1 125 17 17 PRO HD2 H 2.280 0.01 1 126 17 17 PRO HD3 H 2.351 0.01 1 127 18 18 LYS H H 8.296 0.02 1 128 18 18 LYS HA H 4.177 0.01 1 129 18 18 LYS HB2 H 1.749 0.01 2 130 18 18 LYS HB3 H 1.650 0.01 2 131 18 18 LYS HG2 H 1.412 0.01 2 132 18 18 LYS HG3 H 1.330 0.01 2 133 18 18 LYS HD2 H 1.618 0.01 2 134 18 18 LYS HD3 H 1.618 0.01 2 135 18 18 LYS HE2 H 2.942 0.01 2 136 18 18 LYS HE3 H 2.942 0.01 2 137 19 19 GLY H H 8.443 0.02 1 138 19 19 GLY HA2 H 3.979 0.01 2 139 19 19 GLY HA3 H 3.822 0.01 2 140 20 20 LEU H H 8.552 0.02 1 141 20 20 LEU HA H 4.409 0.01 1 142 20 20 LEU HB2 H 1.670 0.01 2 143 20 20 LEU HB3 H 1.670 0.01 2 144 20 20 LEU HG H 1.620 0.01 1 145 20 20 LEU HD1 H 0.951 0.01 2 146 20 20 LEU HD2 H 0.886 0.01 2 147 21 21 VAL H H 8.018 0.02 1 148 21 21 VAL HA H 4.282 0.01 1 149 21 21 VAL HB H 2.285 0.01 1 150 21 21 VAL HG1 H 0.963 0.01 2 151 21 21 VAL HG2 H 0.963 0.01 2 152 22 22 LYS H H 8.371 0.02 1 153 22 22 LYS HA H 4.349 0.01 1 154 22 22 LYS HB2 H 1.830 0.01 2 155 22 22 LYS HB3 H 1.830 0.01 2 156 22 22 LYS HG2 H 1.523 0.01 2 157 22 22 LYS HG3 H 1.428 0.01 2 158 22 22 LYS HD2 H 1.681 0.01 2 159 22 22 LYS HD3 H 1.681 0.01 2 160 23 23 GLY H H 8.919 0.02 1 161 23 23 GLY HA2 H 4.141 0.01 1 162 23 23 GLY HA3 H 3.631 0.01 1 163 24 24 TRP H H 8.079 0.02 1 164 24 24 TRP HA H 5.125 0.01 1 165 24 24 TRP HB2 H 3.384 0.01 1 166 24 24 TRP HB3 H 3.044 0.01 1 167 24 24 TRP HD1 H 7.204 0.01 1 168 24 24 TRP HE1 H 10.28 0.01 1 169 24 24 TRP HE3 H 7.431 0.01 1 170 24 24 TRP HZ2 H 7.441 0.01 1 171 24 24 TRP HZ3 H 7.001 0.01 1 172 24 24 TRP HH2 H 6.946 0.01 1 173 25 25 GLU H H 9.756 0.02 1 174 25 25 GLU HA H 4.912 0.01 1 175 25 25 GLU HB2 H 2.545 0.01 1 176 25 25 GLU HB3 H 2.127 0.01 1 177 25 25 GLU HG2 H 2.242 0.01 2 178 25 25 GLU HG3 H 2.242 0.01 2 179 26 26 LYS H H 8.893 0.02 1 180 26 26 LYS HA H 4.624 0.01 1 181 26 26 LYS HB2 H 1.663 0.01 1 182 26 26 LYS HB3 H 1.441 0.01 1 183 26 26 LYS HG2 H 1.022 0.01 1 184 26 26 LYS HG3 H 0.779 0.01 1 185 26 26 LYS HD2 H 1.205 0.01 2 186 26 26 LYS HD3 H 1.130 0.01 2 187 26 26 LYS HE2 H 2.082 0.01 1 188 26 26 LYS HE3 H 2.003 0.01 1 189 27 27 ARG H H 9.102 0.02 1 190 27 27 ARG HA H 4.722 0.01 1 191 27 27 ARG HB2 H 1.451 0.01 1 192 27 27 ARG HB3 H 0.388 0.01 1 193 27 27 ARG HG2 H 1.502 0.01 1 194 27 27 ARG HG3 H 1.383 0.01 1 195 27 27 ARG HD2 H 2.997 0.01 2 196 27 27 ARG HD3 H 2.737 0.01 2 197 27 27 ARG HE H 7.409 0.01 1 198 28 28 TRP H H 8.426 0.02 1 199 28 28 TRP HA H 4.963 0.01 1 200 28 28 TRP HB2 H 2.856 0.01 1 201 28 28 TRP HB3 H 2.414 0.01 1 202 28 28 TRP HD1 H 6.947 0.01 1 203 28 28 TRP HE1 H 10.04 0.01 1 204 28 28 TRP HE3 H 5.643 0.01 1 205 28 28 TRP HZ2 H 7.389 0.01 1 206 28 28 TRP HZ3 H 6.407 0.01 1 207 28 28 TRP HH2 H 7.068 0.01 1 208 29 29 ASP H H 8.259 0.02 1 209 29 29 ASP HA H 4.346 0.01 1 210 29 29 ASP HB2 H 2.651 0.01 2 211 29 29 ASP HB3 H 2.553 0.01 2 stop_ save_