data_16704 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SPI2 (T7Y) ; _BMRB_accession_number 16704 _BMRB_flat_file_name bmr16704.str _Entry_type original _Submission_date 2010-02-03 _Accession_date 2010-02-03 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Structure of atypical Kazal-type serine proteinase inhibitor solved by NMR spectroscopy' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Nowicka Ursula . . 2 Kludkiewicz Barbara . . 3 Grzelak Krystyna . . 4 Zagorski-Ostoja Wlodzimierz . . 5 Zhukov Igor . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 212 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-08-03 original author . stop_ loop_ _Related_BMRB_accession_number _Relationship 16703 SPI2 16705 SPI2(T7A) stop_ _Original_release_date 2012-08-03 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'High-resolution structure of atypical serine proteinase inhibitors by means of NMR spectroscopy' _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 Nowicka Ursula . . 2 Kludkiewicz Barbara . . 3 Grzelak Krystyna . . 4 Zagorski-Ostoja Wlodzimierz . . 5 Zhukov Igor . . stop_ _Journal_abbreviation 'Not known' _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 'SPI2 (T7Y)' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'SPI2 (T7Y)' $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 'SPI2 (T7Y)' _Molecular_mass 5095.572 _Mol_thiol_state 'all disulfide bound' loop_ _Biological_function 'serine protease inhibitor' stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 45 _Mol_residue_sequence ; EAAVCTYEWDPVCGKDGKTY SNLCWLNEAGVGLDHEGECH HHHHH ; loop_ _Residue_seq_code _Residue_label 1 GLU 2 ALA 3 ALA 4 VAL 5 CYS 6 THR 7 TYR 8 GLU 9 TRP 10 ASP 11 PRO 12 VAL 13 CYS 14 GLY 15 LYS 16 ASP 17 GLY 18 LYS 19 THR 20 TYR 21 SER 22 ASN 23 LEU 24 CYS 25 TRP 26 LEU 27 ASN 28 GLU 29 ALA 30 GLY 31 VAL 32 GLY 33 LEU 34 ASP 35 HIS 36 GLU 37 GLY 38 GLU 39 CYS 40 HIS 41 HIS 42 HIS 43 HIS 44 HIS 45 HIS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-03-26 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 16703 spi2 88.89 45 97.50 97.50 2.36e-18 BMRB 16705 "SPI2 (T7A)" 88.89 45 97.50 97.50 2.39e-18 BMRB 19085 GmSPI_2 86.67 40 97.44 97.44 1.57e-18 PDB 2M5X "Novel Method Of Protein Purification For Structural Research. Example Of Ultra High Resolution Structure Of Spi-2 Inhibitor By " 86.67 40 97.44 97.44 1.57e-18 PDB 4HGU "Crystal Structure Of Galleria Mellonella Silk Protease Inhibitor 2" 86.67 40 97.44 97.44 1.57e-18 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 'greater wax moth' 7137 Eukaryota Metazoa Galleria Mellonella 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 'recombinant technology' . Pichia pastoris . pPICZalfaB 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 $entity 1.0 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' NaCl 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing 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' 'peak picking' stop_ _Details . 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 'structure solution' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model 'Uniform NMR System' _Field_strength 800 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model UnityPlus _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _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_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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' 50 . mM pH 3.5 . pH pressure 1 . 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 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' 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 'SPI2 (T7Y)' _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 GLU HA H 4.010 0.001 1 2 1 1 GLU HB2 H 2.126 0.003 1 3 1 1 GLU HB3 H 2.126 0.003 1 4 1 1 GLU HG2 H 2.514 0.000 1 5 1 1 GLU HG3 H 2.514 0.000 1 6 2 2 ALA H H 8.703 0.001 1 7 2 2 ALA HA H 4.312 0.002 1 8 2 2 ALA HB H 1.361 0.007 1 9 3 3 ALA H H 8.353 0.004 1 10 3 3 ALA HA H 4.295 0.005 1 11 3 3 ALA HB H 1.335 0.003 1 12 4 4 VAL H H 8.101 0.001 1 13 4 4 VAL HA H 3.948 0.004 1 14 4 4 VAL HB H 1.941 0.003 1 15 4 4 VAL HG1 H 0.852 0.001 2 16 4 4 VAL HG2 H 0.816 0.003 2 17 5 5 CYS H H 7.544 0.002 1 18 5 5 CYS HA H 4.516 0.002 1 19 5 5 CYS HB2 H 0.474 0.005 1 20 5 5 CYS HB3 H 1.923 0.004 1 21 6 6 THR H H 8.236 0.004 1 22 6 6 THR HA H 4.595 0.010 1 23 6 6 THR HB H 4.514 0.003 1 24 6 6 THR HG2 H 1.245 0.007 1 25 7 7 TYR H H 8.861 0.003 1 26 7 7 TYR HA H 4.883 0.000 1 27 7 7 TYR HB2 H 3.565 0.004 2 28 7 7 TYR HB3 H 2.790 0.002 2 29 7 7 TYR HD1 H 6.819 0.002 1 30 7 7 TYR HD2 H 6.819 0.002 1 31 7 7 TYR HE1 H 7.263 0.002 1 32 7 7 TYR HE2 H 7.263 0.002 1 33 8 8 GLU H H 8.082 0.002 1 34 8 8 GLU HA H 4.178 0.003 1 35 8 8 GLU HB2 H 2.085 0.002 2 36 8 8 GLU HB3 H 1.997 0.002 2 37 8 8 GLU HG2 H 2.367 0.003 2 38 8 8 GLU HG3 H 2.277 0.003 2 39 9 9 TRP H H 8.839 0.003 1 40 9 9 TRP HA H 4.988 0.004 1 41 9 9 TRP HB2 H 3.384 0.004 1 42 9 9 TRP HB3 H 3.205 0.003 1 43 9 9 TRP HD1 H 7.230 0.003 1 44 9 9 TRP HE1 H 10.257 0.003 1 45 9 9 TRP HE3 H 7.727 0.002 1 46 9 9 TRP HH2 H 7.079 0.003 1 47 9 9 TRP HZ2 H 7.417 0.005 1 48 9 9 TRP HZ3 H 6.952 0.002 1 49 10 10 ASP H H 8.792 0.005 1 50 10 10 ASP HA H 4.701 0.003 1 51 10 10 ASP HB2 H 2.671 0.004 1 52 10 10 ASP HB3 H 2.572 0.002 1 53 11 11 PRO HA H 4.042 0.002 1 54 11 11 PRO HB2 H 0.972 0.003 1 55 11 11 PRO HB3 H 0.571 0.004 1 56 11 11 PRO HD2 H 3.199 0.001 1 57 11 11 PRO HD3 H 1.111 0.002 1 58 11 11 PRO HG2 H 1.508 0.002 1 59 11 11 PRO HG3 H 1.411 0.003 1 60 12 12 VAL H H 8.055 0.003 1 61 12 12 VAL HA H 4.436 0.001 1 62 12 12 VAL HB H 1.825 0.003 1 63 12 12 VAL HG1 H 0.844 0.005 1 64 12 12 VAL HG2 H 0.588 0.003 1 65 13 13 CYS H H 8.442 0.003 1 66 13 13 CYS HA H 5.222 0.001 1 67 13 13 CYS HB2 H 2.384 0.003 1 68 13 13 CYS HB3 H 1.324 0.004 1 69 14 14 GLY H H 9.590 0.003 1 70 14 14 GLY HA2 H 4.658 0.000 1 71 14 14 GLY HA3 H 4.145 0.004 1 72 15 15 LYS H H 8.869 0.004 1 73 15 15 LYS HA H 4.010 0.004 1 74 15 15 LYS HB2 H 1.729 0.005 1 75 15 15 LYS HB3 H 1.995 0.002 1 76 15 15 LYS HD2 H 1.664 0.003 1 77 15 15 LYS HD3 H 1.616 0.004 1 78 15 15 LYS HE2 H 2.988 0.005 1 79 15 15 LYS HE3 H 2.988 0.005 1 80 15 15 LYS HG2 H 1.232 0.003 1 81 15 15 LYS HG3 H 1.232 0.003 1 82 15 15 LYS HZ H 7.567 0.003 1 83 16 16 ASP H H 8.362 0.003 1 84 16 16 ASP HA H 4.404 0.001 1 85 16 16 ASP HB2 H 2.677 0.003 1 86 16 16 ASP HB3 H 2.985 0.005 1 87 17 17 GLY H H 8.260 0.004 1 88 17 17 GLY HA2 H 4.146 0.002 2 89 17 17 GLY HA3 H 3.654 0.003 2 90 18 18 LYS H H 7.917 0.002 1 91 18 18 LYS HA H 4.403 0.001 1 92 18 18 LYS HB2 H 1.402 0.003 1 93 18 18 LYS HB3 H 1.799 0.003 1 94 18 18 LYS HD2 H 1.543 0.001 1 95 18 18 LYS HD3 H 1.448 0.004 1 96 18 18 LYS HE2 H 2.795 0.003 1 97 18 18 LYS HE3 H 2.795 0.003 1 98 18 18 LYS HG2 H 0.929 0.003 1 99 18 18 LYS HG3 H 1.099 0.005 1 100 18 18 LYS HZ H 7.422 0.002 1 101 19 19 THR H H 8.382 0.003 1 102 19 19 THR HA H 4.864 0.000 1 103 19 19 THR HB H 4.040 0.002 1 104 19 19 THR HG2 H 1.162 0.004 1 105 20 20 TYR H H 9.361 0.002 1 106 20 20 TYR HA H 4.501 0.004 1 107 20 20 TYR HB2 H 2.884 0.004 1 108 20 20 TYR HB3 H 2.560 0.003 1 109 20 20 TYR HD1 H 6.981 0.002 1 110 20 20 TYR HD2 H 6.981 0.002 1 111 20 20 TYR HE1 H 7.136 0.004 1 112 20 20 TYR HE2 H 7.136 0.004 1 113 21 21 SER H H 9.116 0.003 1 114 21 21 SER HA H 3.847 0.004 1 115 21 21 SER HB2 H 3.920 0.003 1 116 21 21 SER HB3 H 4.028 0.003 1 117 22 22 ASN H H 7.347 0.002 1 118 22 22 ASN HA H 4.837 0.001 1 119 22 22 ASN HB2 H 3.041 0.003 1 120 22 22 ASN HB3 H 3.416 0.004 1 121 22 22 ASN HD21 H 6.609 0.003 1 122 22 22 ASN HD22 H 8.289 0.003 1 123 23 23 LEU H H 8.862 0.003 1 124 23 23 LEU HA H 3.843 0.004 1 125 23 23 LEU HB2 H 1.660 0.003 1 126 23 23 LEU HB3 H 1.546 0.002 1 127 23 23 LEU HD1 H 0.849 0.002 1 128 23 23 LEU HD2 H 0.907 0.002 1 129 23 23 LEU HG H 1.749 0.003 1 130 24 24 CYS H H 8.157 0.004 1 131 24 24 CYS HA H 4.093 0.005 1 132 24 24 CYS HB2 H 2.702 0.003 1 133 24 24 CYS HB3 H 3.102 0.003 1 134 25 25 TRP H H 7.496 0.002 1 135 25 25 TRP HA H 4.305 0.002 1 136 25 25 TRP HB2 H 3.755 0.005 1 137 25 25 TRP HB3 H 3.208 0.005 1 138 25 25 TRP HD1 H 7.290 0.002 1 139 25 25 TRP HE1 H 9.344 0.003 1 140 25 25 TRP HE3 H 7.806 0.004 1 141 25 25 TRP HH2 H 7.160 0.005 1 142 25 25 TRP HZ2 H 7.292 0.000 1 143 25 25 TRP HZ3 H 6.473 0.005 1 144 26 26 LEU H H 7.292 0.002 1 145 26 26 LEU HA H 2.930 0.002 1 146 26 26 LEU HB2 H 1.751 0.003 1 147 26 26 LEU HB3 H 0.967 0.003 1 148 26 26 LEU HD1 H 0.592 0.003 1 149 26 26 LEU HD2 H 0.346 0.003 1 150 26 26 LEU HG H 1.303 0.004 1 151 27 27 ASN H H 8.424 0.001 1 152 27 27 ASN HA H 4.388 0.002 1 153 27 27 ASN HB2 H 2.759 0.003 1 154 27 27 ASN HB3 H 2.877 0.003 1 155 27 27 ASN HD21 H 7.545 0.001 1 156 27 27 ASN HD22 H 6.602 0.002 1 157 28 28 GLU H H 8.331 0.002 1 158 28 28 GLU HA H 3.999 0.004 1 159 28 28 GLU HB2 H 2.237 0.003 1 160 28 28 GLU HB3 H 2.116 0.002 1 161 28 28 GLU HG2 H 2.496 0.000 1 162 28 28 GLU HG3 H 2.420 0.003 1 163 29 29 ALA H H 7.545 0.002 1 164 29 29 ALA HA H 4.328 0.004 1 165 29 29 ALA HB H 1.667 0.004 1 166 30 30 GLY H H 7.809 0.003 1 167 30 30 GLY HA2 H 3.912 0.001 2 168 30 30 GLY HA3 H 3.827 0.003 2 169 31 31 VAL H H 6.616 0.003 1 170 31 31 VAL HA H 4.076 0.005 1 171 31 31 VAL HB H 1.742 0.002 1 172 31 31 VAL HG1 H 1.087 0.003 1 173 31 31 VAL HG2 H 0.904 0.003 1 174 32 32 GLY H H 8.564 0.003 1 175 32 32 GLY HA2 H 3.896 0.005 1 176 32 32 GLY HA3 H 3.677 0.004 1 177 33 33 LEU H H 8.624 0.002 1 178 33 33 LEU HA H 3.950 0.002 1 179 33 33 LEU HB2 H 1.207 0.002 1 180 33 33 LEU HB3 H 1.791 0.003 1 181 33 33 LEU HD1 H 0.786 0.003 1 182 33 33 LEU HD2 H 0.591 0.002 1 183 33 33 LEU HG H 1.027 0.002 1 184 34 34 ASP H H 9.065 0.002 1 185 34 34 ASP HA H 4.806 0.000 1 186 34 34 ASP HB2 H 2.399 0.005 1 187 34 34 ASP HB3 H 2.005 0.003 1 188 35 35 HIS H H 7.268 0.003 1 189 35 35 HIS HA H 4.894 0.000 1 190 35 35 HIS HB2 H 3.233 0.002 1 191 35 35 HIS HB3 H 3.444 0.003 1 192 35 35 HIS HD2 H 7.181 0.002 1 193 35 35 HIS HE1 H 8.433 0.000 1 194 36 36 GLU H H 9.373 0.003 1 195 36 36 GLU HA H 4.203 0.004 1 196 36 36 GLU HB2 H 2.093 0.001 1 197 36 36 GLU HB3 H 2.250 0.003 1 198 36 36 GLU HG2 H 2.465 0.002 1 199 36 36 GLU HG3 H 2.390 0.002 1 200 37 37 GLY H H 8.193 0.005 1 201 37 37 GLY HA2 H 3.478 0.004 1 202 37 37 GLY HA3 H 4.491 0.004 1 203 38 38 GLU H H 8.211 0.003 1 204 38 38 GLU HA H 3.873 0.004 1 205 38 38 GLU HB2 H 1.845 0.001 1 206 38 38 GLU HB3 H 2.084 0.002 1 207 38 38 GLU HG2 H 2.311 0.003 1 208 38 38 GLU HG3 H 2.311 0.003 1 209 39 39 CYS H H 8.307 0.003 1 210 39 39 CYS HA H 4.406 0.003 1 211 39 39 CYS HB2 H 2.495 0.001 1 212 39 39 CYS HB3 H 2.978 0.004 1 stop_ save_