data_5609 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR structure of [Ala1,15]kalata B1 ; _BMRB_accession_number 5609 _BMRB_flat_file_name bmr5609.str _Entry_type original _Submission_date 2002-12-02 _Accession_date 2002-12-02 _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 Daly N. L. . 2 Clark R. J. . 3 Craik D. J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 128 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2003-08-01 original BMRB . stop_ _Original_release_date 2002-12-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Disulfide Folding Pathways of Cystine Knot Proteins: Tying the Knot within the Circular Backbone of the Cyclotides ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22476988 _PubMed_ID 12482862 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Daly N. L. . 2 Clark R. J. . 3 Craik D. J. . stop_ _Journal_abbreviation 'J. Biol. Chem.' _Journal_volume 278 _Journal_issue 8 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6314 _Page_last 6322 _Year 2003 _Details . loop_ _Keyword 'cyclic peptide' 'cystine knot' 'triple stranded beta sheet' stop_ save_ ################################## # Molecular system description # ################################## save_system_KALATA _Saveframe_category molecular_system _Mol_system_name 'kalata B1' _Abbreviation_common 'kalata B1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'kalata B1' $KALATA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_KALATA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common KALATA _Abbreviation_common KALATA _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 29 _Mol_residue_sequence ; AGETCVGGTCNTPGATCSWP VCTRNGLPV ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLY 3 GLU 4 THR 5 CYS 6 VAL 7 GLY 8 GLY 9 THR 10 CYS 11 ASN 12 THR 13 PRO 14 GLY 15 ALA 16 THR 17 CYS 18 SER 19 TRP 20 PRO 21 VAL 22 CYS 23 THR 24 ARG 25 ASN 26 GLY 27 LEU 28 PRO 29 VAL stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 1N1U 'Nmr Structure Of [ala1,15]kalata B1' 100.00 29 100.00 100.00 1.59e-07 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $KALATA . . . . . . 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 $KALATA 'chemical synthesis' . . . . . 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 $KALATA 1 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 2.6 loop_ _Task collection stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 1.0 loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 750 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label . save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label . save_ save_E-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label . save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.8 . n/a pressure 1 . atm temperature 290 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 0.0 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' DQF-COSY E-COSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'kalata B1' _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 ALA H H 8.578 0.003 1 2 . 1 ALA HA H 4.037 0.003 1 3 . 1 ALA HB H 1.338 0.003 1 4 . 2 GLY H H 8.737 0.003 1 5 . 2 GLY HA2 H 4.063 0.003 2 6 . 2 GLY HA3 H 3.737 0.003 2 7 . 3 GLU H H 7.729 0.003 1 8 . 3 GLU HA H 4.722 0.003 1 9 . 3 GLU HB2 H 2.055 0.003 2 10 . 3 GLU HB3 H 1.847 0.020 2 11 . 3 GLU HG2 H 2.443 0.003 2 12 . 3 GLU HG3 H 2.356 0.003 2 13 . 4 THR H H 8.547 0.003 1 14 . 4 THR HA H 4.714 0.003 1 15 . 4 THR HB H 4.294 0.016 1 16 . 4 THR HG2 H 1.106 0.001 1 17 . 5 CYS H H 8.286 0.003 1 18 . 5 CYS HA H 4.839 0.006 1 19 . 5 CYS HB2 H 3.111 0.003 2 20 . 6 VAL H H 8.604 0.003 1 21 . 6 VAL HA H 4.022 0.003 1 22 . 6 VAL HB H 2.013 0.003 1 23 . 6 VAL HG1 H 0.956 0.014 2 24 . 7 GLY H H 8.972 0.003 1 25 . 7 GLY HA2 H 4.163 0.003 2 26 . 7 GLY HA3 H 3.865 0.003 2 27 . 8 GLY H H 8.324 0.003 1 28 . 8 GLY HA2 H 4.390 0.003 2 29 . 8 GLY HA3 H 3.955 0.003 2 30 . 9 THR H H 7.855 0.003 1 31 . 9 THR HA H 4.712 0.003 1 32 . 9 THR HB H 4.158 0.001 1 33 . 9 THR HG2 H 1.173 0.003 1 34 . 10 CYS H H 8.793 0.003 1 35 . 10 CYS HA H 4.817 0.003 1 36 . 10 CYS HB2 H 2.837 0.003 1 37 . 10 CYS HB3 H 3.242 0.003 1 38 . 11 ASN H H 8.775 0.003 1 39 . 11 ASN HA H 4.627 0.003 1 40 . 11 ASN HB2 H 2.767 0.002 2 41 . 12 THR H H 7.819 0.014 1 42 . 12 THR HA H 4.574 0.002 1 43 . 12 THR HB H 4.021 0.020 1 44 . 12 THR HG2 H 1.209 0.003 1 45 . 13 PRO HA H 4.342 0.003 1 46 . 13 PRO HB2 H 1.915 0.003 1 47 . 13 PRO HB3 H 2.334 0.003 1 48 . 13 PRO HG2 H 2.136 0.003 2 49 . 13 PRO HG3 H 2.008 0.003 2 50 . 13 PRO HD2 H 4.108 0.003 2 51 . 13 PRO HD3 H 3.703 0.003 2 52 . 14 GLY H H 8.891 0.003 1 53 . 14 GLY HA2 H 4.176 0.003 2 54 . 14 GLY HA3 H 3.717 0.006 2 55 . 15 ALA H H 7.768 0.003 1 56 . 15 ALA HA H 4.968 0.003 1 57 . 15 ALA HB H 1.269 0.022 1 58 . 16 THR H H 9.373 0.003 1 59 . 16 THR HA H 4.461 0.003 1 60 . 16 THR HB H 3.997 0.022 1 61 . 16 THR HG2 H 1.124 0.003 1 62 . 17 CYS H H 9.064 0.003 1 63 . 17 CYS HA H 4.691 0.003 1 64 . 17 CYS HB2 H 2.871 0.003 1 65 . 17 CYS HB3 H 3.143 0.003 1 66 . 18 SER H H 8.890 0.003 1 67 . 18 SER HA H 4.685 0.007 1 68 . 18 SER HB2 H 3.849 0.003 2 69 . 18 SER HB3 H 3.677 0.012 2 70 . 19 TRP H H 8.195 0.013 1 71 . 19 TRP HA H 4.155 0.016 1 72 . 19 TRP HB2 H 3.255 0.018 2 73 . 19 TRP HD1 H 7.306 0.022 1 74 . 19 TRP HE3 H 7.502 0.014 1 75 . 19 TRP HE1 H 10.367 0.001 1 76 . 19 TRP HZ2 H 7.562 0.023 1 77 . 20 PRO HA H 3.475 0.003 1 78 . 20 PRO HB2 H 1.703 0.003 1 79 . 20 PRO HB3 H 0.150 0.005 1 80 . 20 PRO HG2 H 1.499 0.022 2 81 . 20 PRO HG3 H 1.407 0.026 2 82 . 20 PRO HD2 H 3.342 0.019 2 83 . 20 PRO HD3 H 3.175 0.021 2 84 . 21 VAL H H 8.108 0.014 1 85 . 21 VAL HA H 4.326 0.020 1 86 . 21 VAL HB H 2.251 0.024 1 87 . 21 VAL HG1 H 0.808 0.007 2 88 . 22 CYS H H 7.928 0.003 1 89 . 22 CYS HA H 5.150 0.019 1 90 . 22 CYS HB2 H 2.916 0.003 1 91 . 22 CYS HB3 H 2.582 0.003 1 92 . 23 THR H H 9.384 0.003 1 93 . 23 THR HA H 5.078 0.003 1 94 . 23 THR HB H 3.643 0.018 1 95 . 23 THR HG2 H 0.913 0.017 1 96 . 24 ARG H H 9.010 0.003 1 97 . 24 ARG HA H 4.630 0.003 1 98 . 24 ARG HB2 H 1.714 0.008 2 99 . 24 ARG HB3 H 1.374 0.001 2 100 . 24 ARG HG2 H 1.497 0.026 2 101 . 24 ARG HG3 H 1.438 0.028 2 102 . 24 ARG HD2 H 3.145 0.002 2 103 . 24 ARG HD3 H 3.039 0.002 2 104 . 24 ARG HE H 7.222 0.002 1 105 . 25 ASN H H 9.637 0.003 1 106 . 25 ASN HA H 4.401 0.003 1 107 . 25 ASN HB2 H 3.075 0.003 2 108 . 25 ASN HB3 H 2.839 0.003 2 109 . 26 GLY H H 8.728 0.003 1 110 . 26 GLY HA2 H 4.202 0.003 2 111 . 26 GLY HA3 H 3.555 0.003 2 112 . 27 LEU H H 7.636 0.003 1 113 . 27 LEU HB2 H 1.751 0.026 2 114 . 27 LEU HB3 H 1.602 0.016 2 115 . 27 LEU HG H 1.608 0.056 1 116 . 27 LEU HD1 H 0.955 0.003 2 117 . 28 PRO HA H 4.504 0.003 1 118 . 28 PRO HB2 H 1.800 0.003 1 119 . 28 PRO HB3 H 2.195 0.003 1 120 . 28 PRO HG2 H 2.139 0.003 2 121 . 28 PRO HG3 H 1.950 0.003 2 122 . 28 PRO HD2 H 3.915 0.003 2 123 . 28 PRO HD3 H 3.666 0.017 2 124 . 29 VAL H H 8.615 0.001 1 125 . 29 VAL HA H 3.970 0.002 1 126 . 29 VAL HB H 1.811 0.020 1 127 . 29 VAL HG1 H 0.827 0.006 2 128 . 29 VAL HG2 H 0.764 0.021 2 stop_ save_