data_16437 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of intermeidate IIa of Leeck-derived tryptase inhibitor, LDTI. ; _BMRB_accession_number 16437 _BMRB_flat_file_name bmr16437.str _Entry_type original _Submission_date 2009-08-03 _Accession_date 2009-08-03 _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 Pantoja-Uceda David . . 2 Santoro Jorge . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 213 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-01-20 update BMRB 'complete entry citation' 2009-11-18 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 16435 'LDTI, apo- form' 16436 'LDTI - IIa' 16438 'LDTI - IIc' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Deciphering the structural basis that guides the oxidative folding of leech-derived tryptase inhibitor.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19820233 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Pantoja-Uceda David . . 2 Arolas Joan L. . 3 Aviles Francesc X. . 4 Santoro Jorge . . 5 Ventura Salvador . . 6 Sommerhoff Christian P. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_name_full 'The Journal of biological chemistry' _Journal_volume 284 _Journal_issue 51 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 35612 _Page_last 35620 _Year 2009 _Details . loop_ _Keyword NMR 'protein folding' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name LDTI_-_IIb _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label LDTI_-_IIb $LDTI_-_IIb stop_ _System_molecular_weight . _System_physical_state intermediate _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function 'tryptase inhibitor' stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_LDTI_-_IIb _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common LDTI_-_IIb _Molecular_mass . _Mol_thiol_state 'free and disulfide bound' loop_ _Biological_function 'tryptase inhibitor' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 44 _Mol_residue_sequence ; KKVCACPKILKPVCGSDGRT YANSCIARCNGVSIKSEGSC PTGI ; loop_ _Residue_seq_code _Residue_label 1 LYS 2 LYS 3 VAL 4 CYS 5 ALA 6 CYS 7 PRO 8 LYS 9 ILE 10 LEU 11 LYS 12 PRO 13 VAL 14 CYS 15 GLY 16 SER 17 ASP 18 GLY 19 ARG 20 THR 21 TYR 22 ALA 23 ASN 24 SER 25 CYS 26 ILE 27 ALA 28 ARG 29 CYS 30 ASN 31 GLY 32 VAL 33 SER 34 ILE 35 LYS 36 SER 37 GLU 38 GLY 39 SER 40 CYS 41 PRO 42 THR 43 GLY 44 ILE stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 BMRB 16435 LDTI 100.00 44 100.00 100.00 3.83e-21 BMRB 16436 LDTI_-_IIa 100.00 44 100.00 100.00 3.83e-21 BMRB 16438 LDTI_-_IIc 100.00 44 100.00 100.00 3.83e-21 PDB 1AN1 "Leech-Derived Tryptase InhibitorTRYPSIN COMPLEX" 100.00 46 100.00 100.00 3.10e-21 PDB 1LDT "Complex Of Leech-Derived Tryptase Inhibitor With Porcine Trypsin" 100.00 46 100.00 100.00 3.10e-21 PDB 2KMO "Solution Structure Of Native Leech-Derived Tryptase Inhibitor, Ldti" 100.00 44 100.00 100.00 3.83e-21 PDB 2KMP "Solution Structure Of Intermeidate Iia Of Leeck-Derived Tryptase Inhibitor, Ldti." 100.00 44 100.00 100.00 3.83e-21 PDB 2KMQ "Solution Structure Of Intermediate Iib Of Leech-Derived Tryptase Inhibitor, Ldti." 100.00 44 100.00 100.00 3.83e-21 PDB 2KMR "Solution Structure Of Intermediate Iic Of Leech-Derived Tryptase Inhibitor, Ldti" 100.00 44 100.00 100.00 3.83e-21 GB AAB33769 "master cell tryptase inhibitor, LDTI [Hirudo medicinalis=medical leeches, Peptide, 46 aa]" 100.00 46 100.00 100.00 3.10e-21 SP P80424 "RecName: Full=Leech-derived tryptase inhibitor C; Short=LDTI-C; Contains: RecName: Full=Leech-derived tryptase inhibitor B; Sho" 100.00 46 100.00 100.00 3.10e-21 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $LDTI_-_IIb 'medicinal leech' 6421 Eukaryota Metazoa Hirudo medicinalis 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 $LDTI_-_IIb 'recombinant technology' . Escherichia coli . pVT102U/a 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 $LDTI_-_IIb 1.7 mM 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $LDTI_-_IIb 1.7 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_NMRView _Saveframe_category software _Name NMRView _Version 5.0.20 loop_ _Vendor _Address _Electronic_address 'Johnson, One Moon Scientific' . . stop_ loop_ _Task 'data analysis' 'peak picking' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 9.0 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . 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_COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 1.7 . pH pressure 1.0 . 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 water H 1 protons ppm 4.7 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_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $NMRView stop_ loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H COSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name LDTI_-_IIb _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 3.937 0.02 1 2 2 2 LYS H H 8.634 0.02 1 3 2 2 LYS HA H 4.309 0.02 1 4 2 2 LYS HB2 H 1.656 0.02 2 5 2 2 LYS HB3 H 1.701 0.02 2 6 2 2 LYS HD2 H 1.609 0.02 2 7 2 2 LYS HD3 H 1.609 0.02 2 8 2 2 LYS HG2 H 1.306 0.02 2 9 2 2 LYS HG3 H 1.349 0.02 2 10 3 3 VAL H H 8.358 0.02 1 11 3 3 VAL HA H 3.981 0.02 1 12 3 3 VAL HB H 1.918 0.02 1 13 3 3 VAL HG1 H 0.808 0.02 2 14 3 3 VAL HG2 H 0.856 0.02 2 15 4 4 CYS H H 8.569 0.02 1 16 4 4 CYS HA H 4.580 0.02 1 17 4 4 CYS HB2 H 2.903 0.02 2 18 4 4 CYS HB3 H 3.041 0.02 2 19 5 5 ALA H H 8.510 0.02 1 20 5 5 ALA HA H 4.293 0.02 1 21 5 5 ALA HB H 1.251 0.02 1 22 6 6 CYS H H 8.262 0.02 1 23 6 6 CYS HA H 4.790 0.02 1 24 6 6 CYS HB2 H 2.747 0.02 2 25 6 6 CYS HB3 H 2.747 0.02 2 26 7 7 PRO HA H 4.445 0.02 1 27 7 7 PRO HB2 H 1.760 0.02 2 28 7 7 PRO HB3 H 2.253 0.02 2 29 7 7 PRO HD2 H 3.760 0.02 2 30 7 7 PRO HD3 H 3.589 0.02 2 31 7 7 PRO HG2 H 1.943 0.02 2 32 7 7 PRO HG3 H 1.973 0.02 2 33 8 8 LYS H H 8.581 0.02 1 34 8 8 LYS HA H 4.196 0.02 1 35 8 8 LYS HB2 H 1.821 0.02 2 36 8 8 LYS HB3 H 1.619 0.02 2 37 9 9 ILE H H 6.998 0.02 1 38 9 9 ILE HA H 4.046 0.02 1 39 9 9 ILE HB H 1.618 0.02 1 40 9 9 ILE HD1 H 0.797 0.02 1 41 9 9 ILE HG13 H 1.005 0.02 2 42 9 9 ILE HG2 H 0.797 0.02 1 43 10 10 LEU H H 8.616 0.02 1 44 10 10 LEU HA H 4.612 0.02 1 45 10 10 LEU HB2 H 1.740 0.02 2 46 10 10 LEU HB3 H 1.740 0.02 2 47 10 10 LEU HD1 H 0.925 0.02 2 48 10 10 LEU HD2 H 0.844 0.02 2 49 10 10 LEU HG H 1.410 0.02 1 50 11 11 LYS H H 8.698 0.02 1 51 11 11 LYS HA H 4.524 0.02 1 52 11 11 LYS HB2 H 1.566 0.02 2 53 11 11 LYS HB3 H 1.766 0.02 2 54 11 11 LYS HG2 H 1.436 0.02 2 55 11 11 LYS HG3 H 1.648 0.02 2 56 12 12 PRO HA H 4.553 0.02 1 57 12 12 PRO HB2 H 1.848 0.02 2 58 12 12 PRO HB3 H 1.806 0.02 2 59 12 12 PRO HD2 H 3.590 0.02 2 60 12 12 PRO HD3 H 3.317 0.02 2 61 12 12 PRO HG2 H 1.449 0.02 2 62 12 12 PRO HG3 H 1.995 0.02 2 63 13 13 VAL H H 8.273 0.02 1 64 13 13 VAL HA H 4.660 0.02 1 65 13 13 VAL HB H 2.110 0.02 1 66 13 13 VAL HG1 H 0.916 0.02 2 67 13 13 VAL HG2 H 0.522 0.02 2 68 14 14 CYS H H 8.691 0.02 1 69 14 14 CYS HA H 5.195 0.02 1 70 14 14 CYS HB2 H 2.543 0.02 2 71 14 14 CYS HB3 H 3.078 0.02 2 72 15 15 GLY H H 9.670 0.02 1 73 15 15 GLY HA2 H 4.741 0.02 2 74 15 15 GLY HA3 H 4.103 0.02 2 75 16 16 SER H H 8.986 0.02 1 76 16 16 SER HA H 3.968 0.02 1 77 16 16 SER HB2 H 3.739 0.02 2 78 16 16 SER HB3 H 3.739 0.02 2 79 17 17 ASP H H 8.117 0.02 1 80 17 17 ASP HA H 4.504 0.02 1 81 17 17 ASP HB2 H 3.066 0.02 2 82 17 17 ASP HB3 H 2.717 0.02 2 83 18 18 GLY H H 8.343 0.02 1 84 18 18 GLY HA2 H 3.687 0.02 2 85 18 18 GLY HA3 H 4.013 0.02 2 86 19 19 ARG H H 7.461 0.02 1 87 19 19 ARG HA H 4.386 0.02 1 88 19 19 ARG HB2 H 1.636 0.02 2 89 19 19 ARG HB3 H 1.288 0.02 2 90 19 19 ARG HD2 H 2.951 0.02 2 91 19 19 ARG HD3 H 2.981 0.02 2 92 19 19 ARG HE H 6.921 0.02 1 93 19 19 ARG HG2 H 1.175 0.02 2 94 19 19 ARG HG3 H 1.175 0.02 2 95 20 20 THR H H 8.285 0.02 1 96 20 20 THR HA H 4.936 0.02 1 97 20 20 THR HB H 3.812 0.02 1 98 20 20 THR HG2 H 1.068 0.02 1 99 21 21 TYR H H 9.145 0.02 1 100 21 21 TYR HA H 4.531 0.02 1 101 21 21 TYR HB2 H 2.387 0.02 2 102 21 21 TYR HB3 H 2.803 0.02 2 103 21 21 TYR HD1 H 7.038 0.02 1 104 21 21 TYR HD2 H 7.038 0.02 1 105 21 21 TYR HE1 H 6.881 0.02 1 106 21 21 TYR HE2 H 6.881 0.02 1 107 22 22 ALA H H 8.861 0.02 1 108 22 22 ALA HA H 3.843 0.02 1 109 22 22 ALA HB H 1.371 0.02 1 110 23 23 ASN H H 7.100 0.02 1 111 23 23 ASN HA H 4.910 0.02 1 112 23 23 ASN HB2 H 2.979 0.02 2 113 23 23 ASN HB3 H 3.266 0.02 2 114 23 23 ASN HD21 H 6.838 0.02 2 115 23 23 ASN HD22 H 6.353 0.02 2 116 24 24 SER H H 9.422 0.02 1 117 24 24 SER HA H 3.905 0.02 1 118 25 25 CYS H H 8.132 0.02 1 119 25 25 CYS HA H 4.110 0.02 1 120 25 25 CYS HB2 H 3.039 0.02 2 121 25 25 CYS HB3 H 2.980 0.02 2 122 26 26 ILE H H 8.022 0.02 1 123 26 26 ILE HA H 3.810 0.02 1 124 26 26 ILE HB H 1.812 0.02 1 125 26 26 ILE HG12 H 1.142 0.02 2 126 26 26 ILE HG13 H 1.230 0.02 2 127 26 26 ILE HG2 H 0.928 0.02 1 128 27 27 ALA H H 7.326 0.02 1 129 27 27 ALA HA H 2.798 0.02 1 130 27 27 ALA HB H 0.887 0.02 1 131 28 28 ARG H H 7.847 0.02 1 132 28 28 ARG HA H 3.947 0.02 1 133 28 28 ARG HB2 H 1.883 0.02 2 134 28 28 ARG HB3 H 1.852 0.02 2 135 28 28 ARG HG2 H 1.704 0.02 2 136 28 28 ARG HG3 H 1.575 0.02 2 137 29 29 CYS H H 8.523 0.02 1 138 29 29 CYS HA H 4.128 0.02 1 139 29 29 CYS HB2 H 3.467 0.02 2 140 29 29 CYS HB3 H 3.271 0.02 2 141 30 30 ASN H H 7.401 0.02 1 142 30 30 ASN HA H 4.537 0.02 1 143 30 30 ASN HB2 H 2.829 0.02 2 144 30 30 ASN HB3 H 2.395 0.02 2 145 30 30 ASN HD21 H 7.363 0.02 2 146 30 30 ASN HD22 H 7.180 0.02 2 147 31 31 GLY H H 7.919 0.02 1 148 31 31 GLY HA2 H 3.731 0.02 2 149 31 31 GLY HA3 H 3.915 0.02 2 150 32 32 VAL H H 7.316 0.02 1 151 32 32 VAL HA H 4.212 0.02 1 152 32 32 VAL HB H 1.838 0.02 1 153 32 32 VAL HG1 H 0.876 0.02 2 154 32 32 VAL HG2 H 0.606 0.02 2 155 33 33 SER H H 8.039 0.02 1 156 33 33 SER HA H 4.378 0.02 1 157 33 33 SER HB2 H 3.794 0.02 2 158 33 33 SER HB3 H 3.769 0.02 2 159 34 34 ILE H H 8.555 0.02 1 160 34 34 ILE HA H 3.867 0.02 1 161 34 34 ILE HB H 1.747 0.02 1 162 34 34 ILE HD1 H 0.647 0.02 1 163 34 34 ILE HG12 H 1.370 0.02 2 164 34 34 ILE HG13 H 0.924 0.02 2 165 34 34 ILE HG2 H 0.768 0.02 1 166 35 35 LYS H H 9.177 0.02 1 167 35 35 LYS HA H 4.243 0.02 1 168 35 35 LYS HB2 H 1.377 0.02 2 169 35 35 LYS HB3 H 1.581 0.02 2 170 35 35 LYS HD2 H 1.281 0.02 2 171 35 35 LYS HD3 H 1.242 0.02 2 172 36 36 SER H H 7.740 0.02 1 173 36 36 SER HA H 4.496 0.02 1 174 36 36 SER HB2 H 3.825 0.02 2 175 36 36 SER HB3 H 3.769 0.02 2 176 37 37 GLU H H 8.608 0.02 1 177 37 37 GLU HA H 4.304 0.02 1 178 37 37 GLU HB2 H 2.154 0.02 2 179 37 37 GLU HB3 H 1.915 0.02 2 180 37 37 GLU HG2 H 2.503 0.02 2 181 37 37 GLU HG3 H 2.408 0.02 2 182 38 38 GLY H H 7.992 0.02 1 183 38 38 GLY HA2 H 3.481 0.02 2 184 38 38 GLY HA3 H 4.222 0.02 2 185 39 39 SER H H 7.776 0.02 1 186 39 39 SER HA H 4.092 0.02 1 187 39 39 SER HB2 H 3.690 0.02 2 188 39 39 SER HB3 H 3.650 0.02 2 189 40 40 CYS H H 8.398 0.02 1 190 40 40 CYS HA H 4.614 0.02 1 191 40 40 CYS HB2 H 2.431 0.02 2 192 40 40 CYS HB3 H 3.032 0.02 2 193 41 41 PRO HA H 4.397 0.02 1 194 41 41 PRO HB2 H 2.216 0.02 2 195 41 41 PRO HB3 H 1.849 0.02 2 196 41 41 PRO HD2 H 3.582 0.02 2 197 41 41 PRO HD3 H 3.688 0.02 2 198 41 41 PRO HG2 H 1.949 0.02 2 199 41 41 PRO HG3 H 1.949 0.02 2 200 42 42 THR H H 8.192 0.02 1 201 42 42 THR HA H 4.171 0.02 1 202 42 42 THR HB H 4.101 0.02 1 203 42 42 THR HG2 H 1.117 0.02 1 204 43 43 GLY H H 8.299 0.02 1 205 43 43 GLY HA2 H 3.889 0.02 2 206 43 43 GLY HA3 H 3.889 0.02 2 207 44 44 ILE H H 7.936 0.02 1 208 44 44 ILE HA H 4.225 0.02 1 209 44 44 ILE HB H 1.837 0.02 1 210 44 44 ILE HD1 H 0.784 0.02 1 211 44 44 ILE HG12 H 1.331 0.02 2 212 44 44 ILE HG13 H 1.101 0.02 2 213 44 44 ILE HG2 H 0.834 0.02 1 stop_ save_