data_17986 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of cyclic gomesin peptide ; _BMRB_accession_number 17986 _BMRB_flat_file_name bmr17986.str _Entry_type original _Submission_date 2011-10-08 _Accession_date 2011-10-08 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Engineering of the gomesin peptide through cyclization improves stability and its structure determination' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 CHAN 'LAI YUE' . . 2 ZHANG MINQUAN V. . 3 HUANG YEN-HUA . . 4 WATERS NORMAN . . 5 BANSAL PARAMJIT S. . 6 CRAIK DAVID J. . 7 DALY NORELLE L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 95 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-04-02 original author . stop_ _Original_release_date 2013-04-02 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Cyclization of the antimicrobial Peptide gomesin with native chemical ligation: influences on stability and bioactivity' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 23426877 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 CHAN 'LAI YUE' . . 2 ZHANG MINQUAN V. . 3 HUANG YEN-HUA . . 4 WATERS NORMAN . . 5 BANSAL PARAMJIT S. . 6 CRAIK DAVID J. . 7 DALY NORELLE L. . stop_ _Journal_abbreviation Chembiochem _Journal_volume 14 _Journal_issue 5 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 617 _Page_last 624 _Year 2013 _Details . loop_ _Keyword 'gomesin peptide' cyclization 'antimicrobial peptide' anticancer antimalaria stability 'native chemical ligation' NMR stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'cyclic gomesin' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'cyclic gomesin' $cyclic_gomesin stop_ _System_molecular_weight . _System_physical_state synthetic _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function antimicrobial antimalaria anticancer stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_cyclic_gomesin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common cyclic_gomesin _Molecular_mass 2199.7 _Mol_thiol_state 'all disulfide bound' loop_ _Biological_function antimicrobial anticancer antimalaria stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence GCRRLCYKQRCVTYCRGR loop_ _Residue_seq_code _Residue_label 1 GLY 2 CYS 3 ARG 4 ARG 5 LEU 6 CYS 7 TYR 8 LYS 9 GLN 10 ARG 11 CYS 12 VAL 13 THR 14 TYR 15 CYS 16 ARG 17 GLY 18 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 1KFP "Solution Structure Of The Antimicrobial 18-Residue Gomesin" 94.44 19 100.00 100.00 2.08e-01 EMBL CAD67587 "gomesin precursor [Acanthoscurria gomesiana]" 94.44 84 100.00 100.00 1.46e-02 SP P82358 "RecName: Full=Gomesin; Flags: Precursor [Acanthoscurria gomesiana]" 94.44 84 100.00 100.00 1.46e-02 stop_ save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single disulfide 'cyclic gomesin' 2 CYS SG 'cyclic gomesin' 15 CYS SG single disulfide 'cyclic gomesin' 6 CYS SG 'cyclic gomesin' 11 CYS SG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $cyclic_gomesin Spiders 6896 Eukaryota Metazoa Aphonopelma . 'cyclic gomesin is a synthetic peptide modified from its native sequence' 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 _Details $cyclic_gomesin 'chemical synthesis' . . . . . 'solid phase peptide synthesis with Boc chemistry' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1mM cyclic gomesin in 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $cyclic_gomesin 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % '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 processing collection stop_ _Details . save_ save_XEASY _Saveframe_category software _Name XEASY _Version . loop_ _Vendor _Address _Electronic_address 'Keller and Wuthrich' . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.0 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'chemical shift calculation' 'data analysis' stop_ _Details . save_ save_MOLPROBITY _Saveframe_category software _Name MOLPROBITY _Version . loop_ _Vendor _Address _Electronic_address Richardson . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version 2K.2 loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'data analysis' 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _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 'Cyclic gomesin is soluble in 90% H20/10% D2O. No aggregation was observed.' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 298 . K pH 5.5 . pH pressure 1 . atm 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 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 'cyclic gomesin' _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 GLY H H 7.892 0.005 1 2 1 1 GLY HA2 H 3.754 0.001 2 3 1 1 GLY HA3 H 4.147 0.001 2 4 2 2 CYS H H 8.330 0.001 1 5 2 2 CYS HA H 5.247 0.001 1 6 2 2 CYS HB2 H 2.531 0.002 2 7 2 2 CYS HB3 H 2.903 0.001 2 8 3 3 ARG H H 8.791 0.001 1 9 3 3 ARG HA H 4.518 0.002 1 10 3 3 ARG HB2 H 1.669 0.001 2 11 3 3 ARG HB3 H 1.729 0.001 2 12 3 3 ARG HG2 H 1.485 0.001 1 13 3 3 ARG HG3 H 1.592 0.001 1 14 3 3 ARG HE H 6.964 0.001 1 15 4 4 ARG H H 8.552 0.001 1 16 4 4 ARG HA H 4.852 0.001 1 17 4 4 ARG HB2 H 1.527 0.003 2 18 4 4 ARG HB3 H 1.650 0.001 2 19 4 4 ARG HG3 H 1.355 0.001 1 20 4 4 ARG HD3 H 2.981 0.005 1 21 4 4 ARG HE H 7.040 0.001 1 22 5 5 LEU H H 8.910 0.001 1 23 5 5 LEU HA H 4.604 0.001 1 24 5 5 LEU HG H 0.917 0.002 1 25 5 5 LEU HD1 H 0.718 0.006 1 26 5 5 LEU HD2 H 0.790 0.004 1 27 6 6 CYS H H 8.735 0.001 1 28 6 6 CYS HA H 5.336 0.066 1 29 6 6 CYS HB2 H 2.663 0.001 2 30 6 6 CYS HB3 H 2.905 0.002 2 31 7 7 TYR H H 8.622 0.001 1 32 7 7 TYR HA H 4.519 0.001 1 33 7 7 TYR HB3 H 2.876 0.001 1 34 7 7 TYR HD1 H 7.069 0.005 1 35 7 7 TYR HD2 H 7.069 0.005 1 36 8 8 LYS H H 8.911 0.001 1 37 8 8 LYS HA H 3.555 0.006 1 38 8 8 LYS HB2 H 1.506 0.001 2 39 8 8 LYS HB3 H 1.645 0.008 2 40 8 8 LYS HD3 H 1.451 0.001 2 41 9 9 GLN H H 8.332 0.001 1 42 9 9 GLN HA H 3.931 0.005 1 43 9 9 GLN HB2 H 2.107 0.005 2 44 9 9 GLN HB3 H 2.195 0.001 2 45 10 10 ARG H H 7.797 0.001 1 46 10 10 ARG HA H 4.521 0.002 1 47 10 10 ARG HB2 H 1.766 0.001 1 48 10 10 ARG HB3 H 1.896 0.001 1 49 10 10 ARG HG2 H 1.442 0.001 1 50 10 10 ARG HG3 H 1.535 0.001 1 51 10 10 ARG HD3 H 3.124 0.001 1 52 10 10 ARG HE H 7.117 0.001 1 53 11 11 CYS H H 8.718 0.001 1 54 11 11 CYS HA H 5.444 0.065 1 55 11 11 CYS HB2 H 2.454 0.001 2 56 11 11 CYS HB3 H 2.917 0.002 2 57 12 12 VAL H H 8.830 0.001 1 58 12 12 VAL HA H 4.310 0.005 1 59 12 12 VAL HB H 1.959 0.005 1 60 12 12 VAL HG1 H 0.688 0.003 1 61 12 12 VAL HG2 H 0.799 0.002 1 62 13 13 THR H H 8.403 0.001 1 63 13 13 THR HA H 4.698 0.001 1 64 13 13 THR HB H 3.865 0.005 1 65 13 13 THR HG2 H 1.013 0.002 1 66 14 14 TYR H H 8.965 0.001 1 67 14 14 TYR HA H 4.720 0.007 1 68 14 14 TYR HB2 H 2.764 0.009 2 69 14 14 TYR HB3 H 2.866 0.009 2 70 14 14 TYR HD1 H 6.718 0.001 1 71 14 14 TYR HD2 H 6.718 0.001 1 72 14 14 TYR HE1 H 6.973 0.001 1 73 14 14 TYR HE2 H 6.973 0.001 1 74 15 15 CYS H H 8.790 0.001 1 75 15 15 CYS HA H 5.072 0.001 1 76 15 15 CYS HB2 H 2.843 0.009 2 77 15 15 CYS HB3 H 3.112 0.002 2 78 16 16 ARG H H 8.167 0.001 1 79 16 16 ARG HA H 4.318 0.007 1 80 16 16 ARG HB2 H 1.599 0.002 2 81 16 16 ARG HB3 H 1.698 0.001 2 82 16 16 ARG HG2 H 1.414 0.003 1 83 16 16 ARG HG3 H 1.471 0.012 1 84 16 16 ARG HD2 H 3.114 0.001 1 85 16 16 ARG HH11 H 6.673 0.001 1 86 16 16 ARG HH12 H 6.972 0.001 1 87 17 17 GLY H H 8.746 0.001 1 88 17 17 GLY HA2 H 3.596 0.001 2 89 17 17 GLY HA3 H 3.937 0.001 2 90 18 18 ARG H H 8.667 0.001 1 91 18 18 ARG HA H 4.182 0.006 1 92 18 18 ARG HB2 H 1.643 0.001 2 93 18 18 ARG HB3 H 1.879 0.003 2 94 18 18 ARG HG3 H 1.552 0.001 1 95 18 18 ARG HD3 H 3.101 0.001 1 stop_ save_