data_19808 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Ginsentides: Characterization, Structure and Application of a New Class of Highly Stable Cystine Knot Peptides in Ginseng ; _BMRB_accession_number 19808 _BMRB_flat_file_name bmr19808.str _Entry_type original _Submission_date 2014-02-20 _Accession_date 2014-02-20 _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 Wang Shujing . . 2 Nguyen 'Kien Truc Giang' . . 3 Luo Shining . . 4 Tam 'James P.' . . 5 Yang Daiwen . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 150 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2015-03-02 original author . stop_ _Original_release_date 2015-03-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Ginsentides: Characterization, Structure and Application of a New Class of Highly Stable Cystine Knot Peptides in Ginseng' _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 Wang Shujing . . 2 Nguyen 'Kien Truc Giang' . . 3 Luo Shining . . 4 Tam 'James P.' . . 5 Yang Daiwen . . 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 Ginsentide _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Ginsentide $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 3065.522 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 31 _Mol_residue_sequence ; CKSGGAWCGFDPHGCCGNCG CLVGFCYGTGC ; loop_ _Residue_seq_code _Residue_label 1 CYS 2 LYS 3 SER 4 GLY 5 GLY 6 ALA 7 TRP 8 CYS 9 GLY 10 PHE 11 ASP 12 PRO 13 HIS 14 GLY 15 CYS 16 CYS 17 GLY 18 ASN 19 CYS 20 GLY 21 CYS 22 LEU 23 VAL 24 GLY 25 PHE 26 CYS 27 TYR 28 GLY 29 THR 30 GLY 31 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-03-16 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 PDB 2ML7 "Ginsentides: Characterization, Structure And Application Of A New Class Of Highly Stable Cystine Knot Peptides In Ginseng" 100.00 31 100.00 100.00 4.83e-11 GB AAX40471 "specific abundant protein 3 [Panax ginseng]" 100.00 121 100.00 100.00 1.29e-12 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 Ginseng 4054 Eukaryota Metazoa Panax ginseng 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 'purified from the natural source' . Panax ginseng . . 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 . mM 'natural abundance' H2O 95 % 'natural abundance' D2O 5 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 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 'data analysis' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_NMRspy _Saveframe_category software _Name NMRspy _Version . loop_ _Vendor _Address _Electronic_address 'Zheng Yu, Xu Yingqi and Yang Daiwen' . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 800 _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_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' 0 . M pH 3.3 . 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 C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na 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_chem_shift_list_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 $chemical_shift_reference_1 _Mol_system_component_name Ginsentide _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 CYS HA H 4.847357 0.01 . 2 1 1 CYS HB2 H 3.130975 0.01 . 3 1 1 CYS HB3 H 3.309318 0.01 . 4 2 2 LYS H H 9.033191 0.01 . 5 2 2 LYS HA H 4.598881 0.01 . 6 2 2 LYS HB2 H 1.77512 0.01 . 7 2 2 LYS HB3 H 1.871894 0.01 . 8 2 2 LYS HG2 H 1.453898 0.01 . 9 2 2 LYS HG3 H 1.503322 0.01 . 10 2 2 LYS HD2 H 1.646088 0.01 . 11 2 2 LYS HD3 H 1.646088 0.01 . 12 2 2 LYS HE2 H 3.127026 0.01 . 13 2 2 LYS HE3 H 3.127026 0.01 . 14 3 3 SER H H 8.440815 0.01 . 15 3 3 SER HA H 4.423428 0.01 . 16 3 3 SER HB2 H 4.014302 0.01 . 17 3 3 SER HB3 H 3.919888 0.01 . 18 4 4 GLY H H 8.500258 0.01 . 19 4 4 GLY HA2 H 3.5918 0.01 . 20 4 4 GLY HA3 H 3.775263 0.01 . 21 5 5 GLY H H 9.344868 0.01 . 22 5 5 GLY HA2 H 3.76303 0.01 . 23 5 5 GLY HA3 H 4.428603 0.01 . 24 6 6 ALA H H 8.090574 0.01 . 25 6 6 ALA HA H 4.628778 0.01 . 26 6 6 ALA HB H 1.566623 0.01 . 27 7 7 TRP H H 8.743641 0.01 . 28 7 7 TRP HA H 4.678346 0.01 . 29 7 7 TRP HB2 H 3.162217 0.01 . 30 7 7 TRP HB3 H 3.195261 0.01 . 31 7 7 TRP HD1 H 6.878975 0.01 . 32 7 7 TRP HE1 H 9.143195 0.01 . 33 7 7 TRP HE3 H 6.893681 0.01 . 34 7 7 TRP HZ2 H 7.09298 0.01 . 35 7 7 TRP HZ3 H 7.016458 0.01 . 36 7 7 TRP HH2 H 7.018236 0.01 . 37 8 8 CYS H H 8.997788 0.01 . 38 8 8 CYS HA H 4.434443 0.01 . 39 8 8 CYS HB2 H 3.340029 0.01 . 40 8 8 CYS HB3 H 2.473782 0.01 . 41 9 9 GLY H H 5.291171 0.01 . 42 9 9 GLY HA2 H 2.928905 0.01 . 43 9 9 GLY HA3 H 2.857732 0.01 . 44 10 10 PHE H H 7.372389 0.01 . 45 10 10 PHE HA H 4.740501 0.01 . 46 10 10 PHE HB2 H 3.390383 0.01 . 47 10 10 PHE HB3 H 2.95608 0.01 . 48 10 10 PHE HD1 H 7.311065 0.01 . 49 10 10 PHE HD2 H 7.311065 0.01 . 50 10 10 PHE HE1 H 7.501991 0.01 . 51 10 10 PHE HE2 H 7.501991 0.01 . 52 10 10 PHE HZ H 7.410478 0.01 . 53 11 11 ASP H H 7.400838 0.01 . 54 11 11 ASP HA H 4.946638 0.01 . 55 11 11 ASP HB2 H 2.57305 0.01 . 56 11 11 ASP HB3 H 2.616929 0.01 . 57 12 12 PRO HA H 4.359326 0.01 . 58 12 12 PRO HB2 H 1.624104 0.01 . 59 12 12 PRO HB3 H 2.147217 0.01 . 60 12 12 PRO HG2 H 3.689361 0.01 . 61 12 12 PRO HG3 H 3.446245 0.01 . 62 12 12 PRO HD2 H 3.747211 0.01 . 63 12 12 PRO HD3 H 3.515652 0.01 . 64 13 13 HIS H H 8.42501 0.01 . 65 13 13 HIS HA H 5.030824 0.01 . 66 13 13 HIS HB2 H 3.573704 0.01 . 67 13 13 HIS HB3 H 3.143334 0.01 . 68 13 13 HIS HD2 H 7.329399 0.01 . 69 13 13 HIS HE1 H 8.657103 0.01 . 70 14 14 GLY H H 7.982467 0.01 . 71 14 14 GLY HA2 H 4.224444 0.01 . 72 14 14 GLY HA3 H 3.720045 0.01 . 73 15 15 CYS H H 8.580532 0.01 . 74 15 15 CYS HA H 4.91438 0.01 . 75 15 15 CYS HB2 H 2.814459 0.01 . 76 15 15 CYS HB3 H 2.814459 0.01 . 77 16 16 CYS H H 9.591428 0.01 . 78 16 16 CYS HA H 4.659463 0.01 . 79 16 16 CYS HB2 H 2.587866 0.01 . 80 16 16 CYS HB3 H 3.392744 0.01 . 81 17 17 GLY H H 8.707606 0.01 . 82 17 17 GLY HA2 H 3.89092 0.01 . 83 17 17 GLY HA3 H 3.813672 0.01 . 84 18 18 ASN H H 8.154426 0.01 . 85 18 18 ASN HA H 4.917527 0.01 . 86 18 18 ASN HB2 H 2.859305 0.01 . 87 18 18 ASN HB3 H 2.989125 0.01 . 88 18 18 ASN HD21 H 6.803405 0.01 . 89 18 18 ASN HD22 H 7.447622 0.01 . 90 19 19 CYS H H 7.826312 0.01 . 91 19 19 CYS HA H 4.248763 0.01 . 92 19 19 CYS HB2 H 2.945065 0.01 . 93 19 19 CYS HB3 H 3.470635 0.01 . 94 20 20 GLY H H 8.459851 0.01 . 95 20 20 GLY HA2 H 3.731772 0.01 . 96 20 20 GLY HA3 H 4.520989 0.01 . 97 21 21 CYS H H 8.66019 0.01 . 98 21 21 CYS HA H 4.785348 0.01 . 99 21 21 CYS HB2 H 2.932476 0.01 . 100 21 21 CYS HB3 H 2.795576 0.01 . 101 22 22 LEU H H 8.921923 0.01 . 102 22 22 LEU HA H 4.620911 0.01 . 103 22 22 LEU HB2 H 1.793216 0.01 . 104 22 22 LEU HB3 H 1.793216 0.01 . 105 22 22 LEU HG H 1.513121 0.01 . 106 22 22 LEU HD1 H 0.904152 0.01 . 107 22 22 LEU HD2 H 0.626418 0.01 . 108 23 23 VAL H H 9.171644 0.01 . 109 23 23 VAL HA H 3.651595 0.01 . 110 23 23 VAL HB H 2.520202 0.01 . 111 23 23 VAL HG1 H 1.050493 0.01 . 112 23 23 VAL HG2 H 0.948999 0.01 . 113 24 24 GLY H H 7.461546 0.01 . 114 24 24 GLY HA2 H 2.674412 0.01 . 115 24 24 GLY HA3 H 3.793359 0.01 . 116 25 25 PHE H H 7.697975 0.01 . 117 25 25 PHE HA H 5.445458 0.01 . 118 25 25 PHE HB2 H 2.813672 0.01 . 119 25 25 PHE HB3 H 2.757811 0.01 . 120 25 25 PHE HD1 H 7.348365 0.01 . 121 25 25 PHE HD2 H 7.348365 0.01 . 122 25 25 PHE HE1 H 7.600615 0.01 . 123 25 25 PHE HE2 H 7.600615 0.01 . 124 25 25 PHE HZ H 7.465956 0.01 . 125 26 26 CYS H H 8.726572 0.01 . 126 26 26 CYS HA H 5.102421 0.01 . 127 26 26 CYS HB2 H 2.849077 0.01 . 128 26 26 CYS HB3 H 3.285098 0.01 . 129 27 27 TYR H H 9.615452 0.01 . 130 27 27 TYR HA H 4.915954 0.01 . 131 27 27 TYR HB2 H 2.900218 0.01 . 132 27 27 TYR HB3 H 3.123664 0.01 . 133 27 27 TYR HD1 H 7.185257 0.01 . 134 27 27 TYR HD2 H 7.185257 0.01 . 135 27 27 TYR HE1 H 6.871737 0.01 . 136 27 27 TYR HE2 H 6.871737 0.01 . 137 28 28 GLY H H 8.015974 0.01 . 138 28 28 GLY HA2 H 4.599667 0.01 . 139 28 28 GLY HA3 H 3.463554 0.01 . 140 29 29 THR H H 8.291014 0.01 . 141 29 29 THR HA H 4.341603 0.01 . 142 29 29 THR HB H 4.170657 0.01 . 143 29 29 THR HG2 H 1.228306 0.01 . 144 30 30 GLY H H 8.670337 0.01 . 145 30 30 GLY HA2 H 3.981257 0.01 . 146 30 30 GLY HA3 H 4.057145 0.01 . 147 31 31 CYS H H 7.410321 0.01 . 148 31 31 CYS HA H 4.690076 0.01 . 149 31 31 CYS HB2 H 3.296756 0.01 . 150 31 31 CYS HB3 H 3.265285 0.01 . stop_ save_