data_36228 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Three-dimensional Solution NMR Structure of KYE28-PEG48 in Microgel ; _BMRB_accession_number 36228 _BMRB_flat_file_name bmr36228.str _Entry_type original _Submission_date 2018-12-27 _Accession_date 2019-01-10 _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 Ilyas H. . . 2 Bhunia A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 140 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2019-01-14 original BMRB . stop_ _Original_release_date 2019-01-10 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Microgels as carriers of antimicrobial peptides - Effects of peptide PEGylation. ; _Citation_status published _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 Nordstrom Randi . . 2 Nystrom Lina . . 3 Ilyas Humaira . . 4 Atreya 'Hanudatta S.' S. . 5 Borro 'Bruno C.' C. . 6 Bhunia Anirban . . 7 Malmsten Martin . . stop_ _Journal_abbreviation 'Colloids Surf. A Physicochem. Eng. Asp.' _Journal_name_full 'Colloids and Surfaces A: Physicochemical and Engineering Aspects' _Journal_volume 565 _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 8 _Page_last 15 _Year 2019 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Heparin cofactor 2' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity_1 $entity_1 stop_ _System_molecular_weight . _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 protein _Name_common 'Heparin cofactor 2' _Molecular_mass 3604.239 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 28 _Mol_residue_sequence ; KYEITTIHNLFRKLTHRLFR RNFGYTLR ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LYS 2 2 TYR 3 3 GLU 4 4 ILE 5 5 THR 6 6 THR 7 7 ILE 8 8 HIS 9 9 ASN 10 10 LEU 11 11 PHE 12 12 ARG 13 13 LYS 14 14 LEU 15 15 THR 16 16 HIS 17 17 ARG 18 18 LEU 19 19 PHE 20 20 ARG 21 21 ARG 22 22 ASN 23 23 PHE 24 24 GLY 25 25 TYR 26 26 THR 27 27 LEU 28 28 ARG 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_1 Human 9606 Eukaryota Metazoa Homo sapiens 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 $entity_1 'chemical synthesis' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM KYE28-PEG48, 55.5 M Water, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version v2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version 3.4 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_software_4 _Saveframe_category software _Name TOPSPIN _Version 3.5 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance III' _Field_strength 700 _Details '700 MHz FT-NMR Spectrometer equipped with cryo-probe,' save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _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' 1 0.01 mM pH 4.52 0.01 pH pressure 1 0.01 atm temperature 298 0.1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_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 0.000 internal direct . . . 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_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '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 $chem_shift_reference_1 _Mol_system_component_name entity_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 4.106 0.000 1 2 1 1 LYS HB2 H 1.819 0.003 2 3 1 1 LYS HB3 H 1.819 0.003 2 4 2 2 TYR H H 8.556 0.003 1 5 2 2 TYR HA H 4.715 0.006 1 6 2 2 TYR HB2 H 3.245 0.003 1 7 2 2 TYR HB3 H 3.138 0.003 1 8 3 3 GLU H H 8.394 0.014 1 9 3 3 GLU HA H 4.351 0.026 1 10 3 3 GLU HB2 H 1.965 0.004 1 11 3 3 GLU HB3 H 1.863 0.000 1 12 3 3 GLU HG2 H 2.237 0.002 2 13 3 3 GLU HG3 H 2.237 0.002 2 14 4 4 ILE H H 8.326 0.001 1 15 4 4 ILE HA H 4.422 0.027 1 16 4 4 ILE HB H 1.633 0.000 1 17 4 4 ILE HG2 H 1.558 0.000 4 18 4 4 ILE HD1 H 0.915 0.001 4 19 5 5 THR H H 8.175 0.016 1 20 5 5 THR HA H 4.344 0.030 1 21 5 5 THR HB H 4.211 0.000 1 22 5 5 THR HG2 H 1.158 0.000 1 23 6 6 THR H H 8.262 0.003 1 24 6 6 THR HA H 4.421 0.001 1 25 6 6 THR HB H 4.280 0.009 1 26 6 6 THR HG2 H 1.207 0.000 1 27 7 7 ILE H H 8.070 0.004 1 28 7 7 ILE HA H 4.253 0.003 1 29 7 7 ILE HB H 1.707 0.028 1 30 7 7 ILE HG2 H 1.545 0.001 4 31 7 7 ILE HD1 H 0.850 0.006 4 32 8 8 HIS H H 8.556 0.003 1 33 8 8 HIS HA H 4.733 0.003 1 34 8 8 HIS HB2 H 3.244 0.031 1 35 8 8 HIS HB3 H 3.138 0.000 1 36 9 9 ASN H H 8.409 0.002 1 37 9 9 ASN HA H 4.802 0.002 1 38 9 9 ASN HB2 H 2.739 0.003 2 39 9 9 ASN HB3 H 2.739 0.003 2 40 10 10 LEU H H 8.318 0.007 1 41 10 10 LEU HA H 4.423 0.011 1 42 10 10 LEU HB2 H 1.628 0.004 2 43 10 10 LEU HB3 H 1.628 0.004 2 44 10 10 LEU HG H 1.5615 0.000 1 45 10 10 LEU HD1 H 0.894 0.001 2 46 10 10 LEU HD2 H 0.894 0.001 2 47 11 11 PHE H H 8.223 0.003 1 48 11 11 PHE HA H 4.597 0.001 1 49 11 11 PHE HB2 H 3.150 0.000 1 50 11 11 PHE HB3 H 3.061 0.002 1 51 12 12 ARG H H 8.254 0.002 1 52 12 12 ARG HA H 4.262 0.081 1 53 12 12 ARG HB2 H 1.751 0.000 2 54 12 12 ARG HB3 H 1.751 0.000 2 55 12 12 ARG HG2 H 1.628 0.000 2 56 12 12 ARG HG3 H 1.628 0.000 2 57 13 13 LYS H H 8.309 0.033 1 58 13 13 LYS HA H 4.168 0.026 1 59 13 13 LYS HB2 H 1.863 0.000 2 60 13 13 LYS HB3 H 1.863 0.000 2 61 13 13 LYS HG2 H 1.563 0.003 2 62 13 13 LYS HG3 H 1.563 0.003 2 63 13 13 LYS HD2 H 1.635 0.000 2 64 13 13 LYS HD3 H 1.635 0.000 2 65 14 14 LEU H H 8.267 0.016 1 66 14 14 LEU HA H 4.420 0.002 1 67 14 14 LEU HB2 H 1.754 0.001 2 68 14 14 LEU HB3 H 1.754 0.001 2 69 14 14 LEU HG H 1.628 0.001 1 70 14 14 LEU HD1 H 0.913 0.003 2 71 14 14 LEU HD2 H 0.913 0.003 2 72 15 15 THR H H 8.141 0.002 1 73 15 15 THR HA H 4.296 0.003 1 74 15 15 THR HB H 4.146 0.006 1 75 15 15 THR HG2 H 1.165 0.002 1 76 16 16 HIS H H 8.467 0.002 1 77 16 16 HIS HA H 4.803 0.015 1 78 16 16 HIS HB2 H 3.254 0.036 1 79 16 16 HIS HB3 H 3.139 0.003 1 80 17 17 ARG H H 8.070 0.081 1 81 17 17 ARG HA H 4.255 0.182 1 82 17 17 ARG HB2 H 1.807 0.002 1 83 17 17 ARG HB3 H 1.699 0.003 1 84 17 17 ARG HG2 H 1.553 0.046 2 85 17 17 ARG HG3 H 1.553 0.046 2 86 18 18 LEU H H 8.337 0.004 1 87 18 18 LEU HA H 4.360 0.004 1 88 18 18 LEU HB2 H 1.680 0.000 2 89 18 18 LEU HB3 H 1.680 0.000 2 90 18 18 LEU HG H 1.549 0.002 1 91 18 18 LEU HD1 H 0.927 0.000 2 92 18 18 LEU HD2 H 0.927 0.000 2 93 19 19 PHE H H 8.374 0.002 1 94 19 19 PHE HA H 4.624 0.000 1 95 19 19 PHE HB2 H 3.070 0.001 1 96 19 19 PHE HB3 H 3.007 0.002 1 97 20 20 ARG H H 8.223 0.024 1 98 20 20 ARG HA H 4.267 0.064 1 99 20 20 ARG HB2 H 1.764 0.029 2 100 20 20 ARG HB3 H 1.764 0.029 2 101 20 20 ARG HG2 H 1.668 0.048 2 102 20 20 ARG HG3 H 1.668 0.048 2 103 21 21 ARG H H 8.339 0.262 1 104 21 21 ARG HA H 4.193 0.068 1 105 21 21 ARG HB2 H 1.686 0.023 2 106 21 21 ARG HB3 H 1.686 0.023 2 107 21 21 ARG HG2 H 1.551 0.011 2 108 21 21 ARG HG3 H 1.551 0.011 2 109 22 22 ASN H H 8.446 0.005 1 110 22 22 ASN HA H 4.661 0.028 1 111 22 22 ASN HB2 H 2.765 0.007 1 112 22 22 ASN HB3 H 2.707 0.005 1 113 23 23 PHE H H 8.241 0.006 1 114 23 23 PHE HA H 4.573 0.005 1 115 23 23 PHE HB2 H 3.110 0.001 1 116 23 23 PHE HB3 H 2.956 0.002 1 117 24 24 GLY H H 8.315 0.002 1 118 24 24 GLY HA2 H 3.883 0.005 1 119 24 24 GLY HA3 H 3.883 0.005 1 120 25 25 TYR H H 7.980 0.003 1 121 25 25 TYR HA H 4.638 0.001 1 122 25 25 TYR HB2 H 3.063 0.001 1 123 25 25 TYR HB3 H 2.970 0.000 1 124 26 26 THR H H 8.127 0.001 1 125 26 26 THR HA H 4.291 0.002 1 126 26 26 THR HB H 4.137 0.003 1 127 26 26 THR HG2 H 1.170 0.002 1 128 27 27 LEU H H 8.337 0.004 1 129 27 27 LEU HA H 4.358 0.001 1 130 27 27 LEU HB2 H 1.680 0.000 2 131 27 27 LEU HB3 H 1.680 0.000 2 132 27 27 LEU HG H 1.562 0.000 1 133 27 27 LEU HD1 H 0.898 0.007 2 134 27 27 LEU HD2 H 0.898 0.007 2 135 28 28 ARG H H 8.072 0.005 1 136 28 28 ARG HA H 4.109 0.000 1 137 28 28 ARG HB2 H 1.811 0.000 2 138 28 28 ARG HB3 H 1.811 0.000 2 139 28 28 ARG HG2 H 1.697 0.000 2 140 28 28 ARG HG3 H 1.697 0.000 2 stop_ loop_ _Atom_shift_assign_ID_ambiguity 17,18 30,31 stop_ save_