data_25725 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of cystein-rich peptide jS1 from Jasminum sambac ; _BMRB_accession_number 25725 _BMRB_flat_file_name bmr25725.str _Entry_type original _Submission_date 2015-07-24 _Accession_date 2015-08-03 _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 Shin Joon . . 2 Kumari Geeta . . 3 Serra Aida . . 4 Nguyen Phuong Q.T . 5 Yoon 'Ho Sup' . . 6 Tam James P . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 151 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2016-10-20 update BMRB 'update entry citation' 2016-07-25 original author 'original release' stop_ _Original_release_date 2016-07-25 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Cysteine-Rich Peptide Family with Unusual Disulfide Connectivity from Jasminum sambac ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 26555361 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kumari Geeta . . 2 Serra Aida . . 3 Shin Joon . . 4 Nguyen Phuong Q.T . 5 Sze 'Siu Kwan' . . 6 Yoon 'Ho Sup' . . 7 Tam James P. . stop_ _Journal_abbreviation 'J. Nat. Prod.' _Journal_volume 78 _Journal_issue 11 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 2791 _Page_last 2799 _Year 2015 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cystein-rich peptide jS1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label entity $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 3132.687 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 27 _Mol_residue_sequence ; QLCLQCRSNSDCNIIWRICR DGCCNVI ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLN 2 2 LEU 3 3 CYS 4 4 LEU 5 5 GLN 6 6 CYS 7 7 ARG 8 8 SER 9 9 ASN 10 10 SER 11 11 ASP 12 12 CYS 13 13 ASN 14 14 ILE 15 15 ILE 16 16 TRP 17 17 ARG 18 18 ILE 19 19 CYS 20 20 ARG 21 21 ASP 22 22 GLY 23 23 CYS 24 24 CYS 25 25 ASN 26 26 VAL 27 27 ILE 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 'Arabian jasmine' 660624 Eukaryota Viridiplantae Jasminum sambac stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_type _Vector_name $entity 'purified from the natural source' . Jasminum sambac . na na 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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $entity . mM 0.7 1.0 'natural abundance' H2O 90 % . . 'natural abundance' D2O 10 % . . [U-2H] 'sodium phosphate' 20 mM . . 'natural abundance' 'sodium chloride' 50 mM . . 'natural abundance' 'sodium azide' 0.01 '% w/v' . . 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $entity . mM 0.7 1.0 'natural abundance' D2O 100 % . . [U-2H] 'sodium phosphate' 20 mM . . 'natural abundance' 'sodium chloride' 50 mM . . 'natural abundance' 'sodium azide' 0.01 '% w/v' . . 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ 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_NMRDraw _Saveframe_category software _Name NMRDraw _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 'data analysis' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version . loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'geometry optimization' refinement 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_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _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_2 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _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 7.0 . 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 TOCSY' '2D DQF-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 entity _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 GLN HA H 4.265 0.020 1 2 1 1 GLN HB2 H 1.965 0.020 2 3 1 1 GLN HB3 H 1.938 0.020 2 4 1 1 GLN HG2 H 2.437 0.020 2 5 1 1 GLN HG3 H 2.333 0.020 2 6 2 2 LEU H H 8.217 0.020 1 7 2 2 LEU HA H 4.247 0.020 1 8 2 2 LEU HB2 H 1.498 0.020 2 9 2 2 LEU HB3 H 1.498 0.020 2 10 2 2 LEU HD1 H 0.823 0.020 2 11 2 2 LEU HD2 H 0.775 0.020 2 12 3 3 CYS H H 8.312 0.020 1 13 3 3 CYS HA H 4.602 0.020 1 14 3 3 CYS HB2 H 3.094 0.020 2 15 3 3 CYS HB3 H 3.094 0.020 2 16 4 4 LEU H H 9.169 0.020 1 17 4 4 LEU HA H 4.379 0.020 1 18 4 4 LEU HB2 H 1.519 0.020 2 19 4 4 LEU HB3 H 1.395 0.020 2 20 4 4 LEU HD1 H 0.832 0.020 2 21 4 4 LEU HD2 H 0.757 0.020 2 22 5 5 GLN H H 8.145 0.020 1 23 5 5 GLN HA H 4.575 0.020 1 24 5 5 GLN HB2 H 1.943 0.020 2 25 5 5 GLN HB3 H 1.905 0.020 2 26 5 5 GLN HG2 H 2.390 0.020 2 27 5 5 GLN HG3 H 2.340 0.020 2 28 5 5 GLN HE21 H 7.505 0.020 2 29 5 5 GLN HE22 H 6.744 0.020 2 30 6 6 CYS H H 7.921 0.020 1 31 6 6 CYS HA H 4.769 0.020 1 32 6 6 CYS HB2 H 3.224 0.020 2 33 6 6 CYS HB3 H 3.031 0.020 2 34 7 7 ARG H H 9.480 0.020 1 35 7 7 ARG HA H 4.384 0.020 1 36 7 7 ARG HB2 H 1.852 0.020 2 37 7 7 ARG HB3 H 1.744 0.020 2 38 7 7 ARG HG2 H 1.603 0.020 2 39 7 7 ARG HG3 H 1.603 0.020 2 40 7 7 ARG HD2 H 3.135 0.020 2 41 7 7 ARG HD3 H 3.135 0.020 2 42 8 8 SER H H 8.126 0.020 1 43 8 8 SER HA H 4.625 0.020 1 44 8 8 SER HB2 H 4.031 0.020 2 45 8 8 SER HB3 H 3.812 0.020 2 46 9 9 ASN HA H 4.177 0.020 1 47 9 9 ASN HB2 H 3.061 0.020 2 48 9 9 ASN HB3 H 2.890 0.020 2 49 9 9 ASN HD21 H 7.638 0.020 2 50 9 9 ASN HD22 H 7.003 0.020 2 51 10 10 SER HB2 H 4.177 0.020 2 52 10 10 SER HB3 H 3.796 0.020 2 53 11 11 ASP H H 7.453 0.020 1 54 11 11 ASP HA H 4.655 0.020 1 55 11 11 ASP HB2 H 3.053 0.020 2 56 11 11 ASP HB3 H 2.756 0.020 2 57 12 12 CYS H H 7.506 0.020 1 58 12 12 CYS HA H 4.939 0.020 1 59 12 12 CYS HB2 H 2.774 0.020 2 60 12 12 CYS HB3 H 2.774 0.020 2 61 13 13 ASN H H 7.738 0.020 1 62 13 13 ASN HA H 4.893 0.020 1 63 13 13 ASN HB2 H 3.071 0.020 2 64 13 13 ASN HB3 H 2.772 0.020 2 65 13 13 ASN HD21 H 7.775 0.020 2 66 13 13 ASN HD22 H 6.334 0.020 2 67 14 14 ILE H H 7.546 0.020 1 68 14 14 ILE HA H 3.903 0.020 1 69 14 14 ILE HB H 1.845 0.020 1 70 14 14 ILE HG12 H 1.325 0.020 2 71 14 14 ILE HG13 H 1.155 0.020 2 72 14 14 ILE HG2 H 0.850 0.020 1 73 14 14 ILE HD1 H 0.794 0.020 1 74 15 15 ILE H H 7.658 0.020 1 75 15 15 ILE HA H 3.824 0.020 1 76 15 15 ILE HB H 1.383 0.020 1 77 15 15 ILE HG12 H 1.086 0.020 2 78 15 15 ILE HG13 H 0.826 0.020 2 79 15 15 ILE HG2 H 0.531 0.020 1 80 15 15 ILE HD1 H 0.120 0.020 1 81 16 16 TRP H H 7.898 0.020 1 82 16 16 TRP HA H 4.446 0.020 1 83 16 16 TRP HB2 H 2.993 0.020 2 84 16 16 TRP HB3 H 2.534 0.020 2 85 16 16 TRP HD1 H 7.083 0.020 1 86 16 16 TRP HE1 H 10.181 0.020 1 87 16 16 TRP HE3 H 7.477 0.020 1 88 16 16 TRP HZ2 H 7.375 0.020 1 89 16 16 TRP HZ3 H 7.095 0.020 1 90 16 16 TRP HH2 H 7.137 0.020 1 91 17 17 ARG H H 7.502 0.020 1 92 17 17 ARG HA H 4.595 0.020 1 93 17 17 ARG HB2 H 1.777 0.020 2 94 17 17 ARG HB3 H 1.710 0.020 2 95 17 17 ARG HG2 H 1.683 0.020 2 96 17 17 ARG HG3 H 1.529 0.020 2 97 17 17 ARG HD2 H 3.095 0.020 2 98 17 17 ARG HD3 H 3.074 0.020 2 99 18 18 ILE H H 8.342 0.020 1 100 18 18 ILE HA H 4.132 0.020 1 101 18 18 ILE HB H 1.637 0.020 1 102 18 18 ILE HG12 H 1.244 0.020 2 103 18 18 ILE HG13 H 1.177 0.020 2 104 18 18 ILE HG2 H 0.686 0.020 1 105 18 18 ILE HD1 H 0.635 0.020 1 106 19 19 CYS H H 8.882 0.020 1 107 19 19 CYS HA H 4.629 0.020 1 108 19 19 CYS HB2 H 2.757 0.020 2 109 19 19 CYS HB3 H 2.557 0.020 2 110 20 20 ARG H H 8.565 0.020 1 111 20 20 ARG HA H 4.488 0.020 1 112 20 20 ARG HB2 H 1.614 0.020 2 113 20 20 ARG HB3 H 1.549 0.020 2 114 20 20 ARG HG2 H 1.456 0.020 2 115 20 20 ARG HG3 H 1.378 0.020 2 116 20 20 ARG HD2 H 3.159 0.020 2 117 20 20 ARG HD3 H 3.036 0.020 2 118 20 20 ARG HE H 7.795 0.020 1 119 21 21 ASP H H 9.233 0.020 1 120 21 21 ASP HA H 4.159 0.020 1 121 21 21 ASP HB2 H 2.815 0.020 2 122 21 21 ASP HB3 H 2.540 0.020 2 123 22 22 GLY H H 8.001 0.020 1 124 22 22 GLY HA2 H 4.076 0.020 2 125 22 22 GLY HA3 H 3.905 0.020 2 126 23 23 CYS H H 7.582 0.020 1 127 23 23 CYS HA H 5.343 0.020 1 128 23 23 CYS HB2 H 3.213 0.020 2 129 23 23 CYS HB3 H 2.662 0.020 2 130 24 24 CYS H H 9.137 0.020 1 131 24 24 CYS HA H 4.934 0.020 1 132 24 24 CYS HB2 H 3.383 0.020 2 133 24 24 CYS HB3 H 2.668 0.020 2 134 25 25 ASN H H 9.974 0.020 1 135 25 25 ASN HA H 4.904 0.020 1 136 25 25 ASN HB2 H 2.843 0.020 2 137 25 25 ASN HB3 H 2.514 0.020 2 138 25 25 ASN HD21 H 7.302 0.020 2 139 25 25 ASN HD22 H 7.068 0.020 2 140 26 26 VAL H H 8.599 0.020 1 141 26 26 VAL HA H 4.188 0.020 1 142 26 26 VAL HB H 1.980 0.020 1 143 26 26 VAL HG1 H 0.891 0.020 2 144 26 26 VAL HG2 H 0.833 0.020 2 145 27 27 ILE H H 7.300 0.020 1 146 27 27 ILE HA H 4.018 0.020 1 147 27 27 ILE HB H 1.682 0.020 1 148 27 27 ILE HG12 H 1.378 0.020 2 149 27 27 ILE HG13 H 1.106 0.020 2 150 27 27 ILE HG2 H 0.790 0.020 1 151 27 27 ILE HD1 H 0.765 0.020 1 stop_ save_