data_36109 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransferase Domain (PSTD) of the Polysialyltransferase ST8Sia IV ; _BMRB_accession_number 36109 _BMRB_flat_file_name bmr36109.str _Entry_type original _Submission_date 2017-07-23 _Accession_date 2017-12-25 _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 Lu B. . . 2 Liao S. M. . 3 Huang J. M. . 4 Lu Z. L. . 5 Chen D. . . 6 Liu X. H. . 7 Zhou G. P. . 8 Huang R. B. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 132 "13C chemical shifts" 79 "15N chemical shifts" 19 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-01-02 original BMRB . stop_ loop_ _Related_BMRB_accession_number _Relationship 36110 ; NMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransferase Domain (PSTD) of the Polysialyltransferase ST8Sia IV in the Presence of Polysialic Acid (PolySia) ; stop_ _Original_release_date 2017-12-25 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR-Based Model of the 22 Amino Acid Peptide in Polysialyltransferase Domain (PSTD) of the Polysialyltransferase ST8Sia IV ; _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 Lu B. . . 2 Liao S. M. . 3 Chen D. . . 4 Liu X. H. . 5 Zhou G. P. . 6 Huang R. B. . stop_ _Journal_abbreviation . _Journal_volume . _Journal_issue . _Journal_CSD 0353 _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 '22AA-PSTD peptide (E.C.2.4.99.-)' _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 entity_1 _Molecular_mass 2624.181 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; LRLIHAVRGYWLTNKVPIKR PS ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 LEU 2 2 ARG 3 3 LEU 4 4 ILE 5 5 HIS 6 6 ALA 7 7 VAL 8 8 ARG 9 9 GLY 10 10 TYR 11 11 TRP 12 12 LEU 13 13 THR 14 14 ASN 15 15 LYS 16 16 VAL 17 17 PRO 18 18 ILE 19 19 LYS 20 20 ARG 21 21 PRO 22 22 SER 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 '1.0 mM 22AA-PSTD peptide, 40 % trifluoroethanol-d3, trifluoroethanol/water' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1.0 mM 'natural abundance' trifluoroethanol-d3 40 % [U-2H] H2O 60 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name ARIA _Version 2.3.1 loop_ _Vendor _Address _Electronic_address "Linge, O'Donoghue and Nilges" . . stop_ loop_ _Task 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name Analysis _Version 2.4 loop_ _Vendor _Address _Electronic_address CCPN . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name CNS _Version 1.2.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_4 _Saveframe_category software _Name NMRPipe _Version 8.9 loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Agilent _Model DD2 _Field_strength 800 _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-13C_HSQC_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _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_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' 0 . mM pH 6.7 . pH pressure 1 . atm temperature 298 . 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 C 13 'methyl protons' ppm 0.000 internal indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.000 internal direct . . . 1.0 DSS N 15 'methyl protons' ppm 0.000 internal indirect . . . 0.101329118 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-15N HSQC' '2D 1H-13C HSQC' '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 $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 LEU HA H 3.802 0.002 1 2 1 1 LEU HB2 H 1.698 0.003 2 3 1 1 LEU HB3 H 1.595 0.003 2 4 1 1 LEU HD1 H 0.993 0.001 2 5 1 1 LEU HD2 H 0.951 0.0 2 6 1 1 LEU CA C 55.331 . 1 7 1 1 LEU CB C 44.993 0.0 1 8 1 1 LEU CD1 C 24.138 . 2 9 1 1 LEU CD2 C 23.479 . 2 10 2 2 ARG HA H 4.370 0.003 1 11 2 2 ARG HB2 H 1.940 0.004 2 12 2 2 ARG HB3 H 1.866 0.003 2 13 2 2 ARG HG2 H 1.728 0.004 2 14 2 2 ARG HG3 H 1.813 0.003 2 15 2 2 ARG HD2 H 3.238 0.002 1 16 2 2 ARG CA C 57.336 . 1 17 2 2 ARG CD C 43.391 . 1 18 3 3 LEU H H 7.994 0.003 1 19 3 3 LEU HA H 4.257 0.002 1 20 3 3 LEU HB2 H 1.652 0.002 1 21 3 3 LEU HG H 1.792 0.001 1 22 3 3 LEU HD1 H 0.925 0.01 2 23 3 3 LEU HD2 H 0.961 0.006 2 24 3 3 LEU CA C 57.151 . 1 25 3 3 LEU CB C 42.327 . 1 26 3 3 LEU N N 120.602 . 1 27 4 4 ILE H H 7.484 0.001 1 28 4 4 ILE HA H 3.938 0.001 1 29 4 4 ILE HB H 1.863 0.002 1 30 4 4 ILE HG12 H 1.234 0.003 2 31 4 4 ILE HG13 H 1.449 0.005 2 32 4 4 ILE HG2 H 0.813 0.003 1 33 4 4 ILE HD1 H 0.890 0.004 1 34 4 4 ILE CA C 63.063 . 1 35 4 4 ILE CB C 37.958 . 1 36 4 4 ILE CG1 C 28.159 . 1 37 4 4 ILE CG2 C 16.822 . 1 38 4 4 ILE CD1 C 12.391 . 1 39 4 4 ILE N N 116.491 . 1 40 5 5 HIS H H 7.602 0.002 1 41 5 5 HIS HA H 4.424 0.001 1 42 5 5 HIS HB2 H 3.194 0.001 1 43 5 5 HIS HD2 H 7.001 0.002 1 44 5 5 HIS HE1 H 7.730 0.003 1 45 5 5 HIS CA C 58.844 . 1 46 5 5 HIS CB C 30.641 . 1 47 5 5 HIS CD2 C 118.645 . 1 48 5 5 HIS CE1 C 138.161 . 1 49 5 5 HIS N N 119.099 . 1 50 6 6 ALA H H 7.925 0.002 1 51 6 6 ALA HA H 4.251 0.004 1 52 6 6 ALA HB H 1.540 0.003 1 53 6 6 ALA CA C 54.614 . 1 54 6 6 ALA CB C 18.031 . 1 55 6 6 ALA N N 122.609 . 1 56 7 7 VAL H H 8.134 0.002 1 57 7 7 VAL HA H 3.863 0.001 1 58 7 7 VAL HB H 2.171 0.001 1 59 7 7 VAL HG1 H 1.051 0.002 2 60 7 7 VAL HG2 H 0.958 0.004 2 61 7 7 VAL CA C 65.562 . 1 62 7 7 VAL CB C 32.148 . 1 63 7 7 VAL CG1 C 21.271 . 2 64 7 7 VAL CG2 C 20.598 . 2 65 7 7 VAL N N 118.005 . 1 66 8 8 ARG H H 8.187 0.001 1 67 8 8 ARG HA H 4.175 0.001 1 68 8 8 ARG HB2 H 1.945 0.002 2 69 8 8 ARG HB3 H 1.863 0.003 2 70 8 8 ARG HG2 H 1.700 0.004 2 71 8 8 ARG HG3 H 1.860 0.002 2 72 8 8 ARG HD2 H 3.191 0.001 1 73 8 8 ARG HE H 7.119 0.002 1 74 8 8 ARG CA C 59.084 . 1 75 8 8 ARG CG C 27.542 0.002 1 76 8 8 ARG CD C 43.435 . 1 77 8 8 ARG N N 119.358 . 1 78 9 9 GLY H H 8.137 0.003 1 79 9 9 GLY HA2 H 3.864 0.002 1 80 9 9 GLY CA C 46.670 . 1 81 9 9 GLY N N 108.686 . 1 82 10 10 TYR H H 8.125 0.004 1 83 10 10 TYR HA H 4.240 0.003 1 84 10 10 TYR HB2 H 3.172 0.005 2 85 10 10 TYR HB3 H 3.138 0.004 2 86 10 10 TYR HD1 H 6.897 0.001 1 87 10 10 TYR HD2 H 6.897 0.001 1 88 10 10 TYR HE1 H 6.662 0.001 1 89 10 10 TYR HE2 H 6.662 0.001 1 90 10 10 TYR CA C 61.059 . 1 91 10 10 TYR CB C 38.151 0.001 1 92 10 10 TYR CD1 C 133.013 . 1 93 10 10 TYR CD2 C 133.013 . 1 94 10 10 TYR CE1 C 118.019 . 1 95 10 10 TYR CE2 C 118.019 . 1 96 10 10 TYR N N 122.732 . 1 97 11 11 TRP H H 8.288 0.003 1 98 11 11 TRP HA H 4.394 0.001 1 99 11 11 TRP HB2 H 3.425 0.002 2 100 11 11 TRP HB3 H 3.470 0.002 2 101 11 11 TRP HD1 H 7.277 0.0 1 102 11 11 TRP HE1 H 9.767 0.001 1 103 11 11 TRP HE3 H 7.622 0.001 1 104 11 11 TRP HZ2 H 7.493 0.009 1 105 11 11 TRP HZ3 H 7.158 0.003 1 106 11 11 TRP HH2 H 7.252 0.003 1 107 11 11 TRP CA C 60.026 . 1 108 11 11 TRP CB C 28.967 0.003 1 109 11 11 TRP CD1 C 126.517 . 1 110 11 11 TRP CE3 C 120.534 . 1 111 11 11 TRP CZ2 C 114.479 . 1 112 11 11 TRP CZ3 C 121.905 . 1 113 11 11 TRP CH2 C 124.543 . 1 114 11 11 TRP N N 120.737 . 1 115 11 11 TRP NE1 N 126.854 . 1 116 12 12 LEU H H 8.271 0.004 1 117 12 12 LEU HA H 4.171 0.002 1 118 12 12 LEU HB2 H 1.871 0.004 2 119 12 12 LEU HB3 H 1.636 0.003 2 120 12 12 LEU HG H 1.795 0.002 1 121 12 12 LEU HD1 H 0.944 0.004 1 122 12 12 LEU CA C 57.211 . 1 123 12 12 LEU CB C 42.443 . 1 124 12 12 LEU CG C 27.185 . 1 125 12 12 LEU N N 118.607 . 1 126 13 13 THR H H 7.751 0.002 1 127 13 13 THR HA H 4.223 0.003 1 128 13 13 THR HB H 4.286 0.003 1 129 13 13 THR HG2 H 1.268 0.002 1 130 13 13 THR CA C 63.562 . 1 131 13 13 THR CB C 69.874 . 1 132 13 13 THR CG2 C 21.075 . 1 133 13 13 THR N N 109.374 . 1 134 14 14 ASN H H 7.812 0.001 1 135 14 14 ASN HA H 4.659 . 1 136 14 14 ASN HB2 H 2.640 0.003 2 137 14 14 ASN HB3 H 2.556 0.002 2 138 14 14 ASN HD21 H 7.058 0.001 1 139 14 14 ASN HD22 H 6.431 0.001 1 140 14 14 ASN CA C 54.043 . 1 141 14 14 ASN CB C 39.236 0.003 1 142 14 14 ASN N N 118.658 . 1 143 15 15 LYS H H 8.002 0.002 1 144 15 15 LYS HA H 4.318 0.001 1 145 15 15 LYS HB2 H 1.820 0.002 2 146 15 15 LYS HB3 H 1.730 0.003 2 147 15 15 LYS HG2 H 1.315 0.002 1 148 15 15 LYS HD2 H 1.594 0.007 2 149 15 15 LYS HD3 H 1.590 0.007 2 150 15 15 LYS HE2 H 2.940 0.002 2 151 15 15 LYS HE3 H 2.884 0.003 2 152 15 15 LYS CA C 56.180 . 1 153 15 15 LYS CB C 32.772 . 1 154 15 15 LYS CG C 24.413 . 1 155 15 15 LYS CD C 28.553 . 1 156 15 15 LYS CE C 42.238 0.001 1 157 15 15 LYS N N 119.237 . 1 158 16 16 VAL H H 7.695 0.001 1 159 16 16 VAL HA H 4.390 0.001 1 160 16 16 VAL HB H 2.111 0.002 1 161 16 16 VAL HG1 H 0.978 0.002 2 162 16 16 VAL HG2 H 0.966 0.008 2 163 16 16 VAL CA C 60.026 . 1 164 16 16 VAL CB C 32.769 . 1 165 16 16 VAL CG1 C 20.823 . 1 166 16 16 VAL CG2 C 20.823 . 1 167 16 16 VAL N N 119.663 . 1 168 17 17 PRO HA H 4.510 0.001 1 169 17 17 PRO HB2 H 2.031 0.001 2 170 17 17 PRO HB3 H 2.191 0.001 2 171 17 17 PRO HG2 H 2.031 0.002 1 172 17 17 PRO HD2 H 3.656 0.002 2 173 17 17 PRO HD3 H 3.851 0.003 2 174 17 17 PRO CA C 63.401 . 1 175 17 17 PRO CB C 31.163 0.021 1 176 17 17 PRO CG C 27.140 . 1 177 17 17 PRO CD C 50.768 0.018 1 178 18 18 ILE H H 7.628 0.001 1 179 18 18 ILE HA H 4.175 0.002 1 180 18 18 ILE HB H 1.836 0.003 1 181 18 18 ILE HG12 H 1.173 0.002 2 182 18 18 ILE HG13 H 1.503 0.003 2 183 18 18 ILE HG2 H 0.924 0.01 1 184 18 18 ILE HD1 H 0.897 0.006 1 185 18 18 ILE CA C 61.122 . 1 186 18 18 ILE CB C 39.351 . 1 187 18 18 ILE CG1 C 27.186 0.037 1 188 18 18 ILE CG2 C 17.098 . 1 189 18 18 ILE CD1 C 12.391 . 1 190 18 18 ILE N N 119.144 . 1 191 19 19 LYS H H 7.977 0.001 1 192 19 19 LYS HA H 4.411 0.003 1 193 19 19 LYS HB2 H 1.840 0.005 2 194 19 19 LYS HB3 H 1.743 0.002 2 195 19 19 LYS HG2 H 1.438 0.003 1 196 19 19 LYS HD2 H 1.714 0.003 1 197 19 19 LYS HE2 H 3.016 0.002 1 198 19 19 LYS CA C 55.744 . 1 199 19 19 LYS CB C 33.259 0.035 1 200 19 19 LYS CG C 24.551 . 1 201 19 19 LYS CD C 29.037 . 1 202 19 19 LYS CE C 42.193 . 1 203 19 19 LYS N N 124.190 . 1 204 20 20 ARG H H 8.212 0.001 1 205 20 20 ARG HA H 4.661 0.001 1 206 20 20 ARG HB2 H 1.795 0.004 2 207 20 20 ARG HB3 H 1.930 0.003 2 208 20 20 ARG HG2 H 1.725 0.002 1 209 20 20 ARG HD2 H 3.236 0.001 1 210 20 20 ARG HE H 7.248 0.0 1 211 20 20 ARG CA C 54.043 . 1 212 20 20 ARG CD C 43.373 . 1 213 20 20 ARG N N 123.337 . 1 214 21 21 PRO HA H 4.482 0.001 1 215 21 21 PRO HB2 H 2.329 0.003 2 216 21 21 PRO HB3 H 2.046 0.005 2 217 21 21 PRO HG2 H 2.111 0.004 1 218 21 21 PRO HD2 H 3.833 0.003 2 219 21 21 PRO HD3 H 3.689 0.002 2 220 21 21 PRO CA C 63.704 . 1 221 21 21 PRO CB C 31.828 0.019 1 222 21 21 PRO CG C 27.148 . 1 223 21 21 PRO CD C 50.563 . 1 224 22 22 SER H H 7.745 0.002 1 225 22 22 SER HA H 4.289 0.002 1 226 22 22 SER HB2 H 3.909 0.002 2 227 22 22 SER HB3 H 3.907 0.001 2 228 22 22 SER CA C 59.875 . 1 229 22 22 SER CB C 65.117 . 1 230 22 22 SER N N 120.442 . 1 stop_ save_