data_36038 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; VG13P structure in LPS ; _BMRB_accession_number 36038 _BMRB_flat_file_name bmr36038.str _Entry_type original _Submission_date 2016-12-04 _Accession_date 2016-06-07 _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 Datta A. . . 2 Bhunia A. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 68 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2017-06-20 original BMRB . stop_ _Original_release_date 2017-06-08 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Structural and Dynamic Insights into a Glycine-Mediated Short Analogue of a Designed Peptide in Lipopolysaccharide Micelles: Correlation Between Compact Structure and Anti-Endotoxin Activity. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28168875 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Datta A. . . 2 Jaiswal N. . . 3 Ilyas H. . . 4 Debnath S. . . 5 Biswas K. . . 6 Kumar D. . . 7 Bhunia A. . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 56 _Journal_issue 9 _Journal_ASTM BICHAW _Journal_ISSN 1520-4995 _Journal_CSD 0033 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1348 _Page_last 1362 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'analogue peptide VG13P' _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 1449.745 _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence ; VARGWGRKCPLFG ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 VAL 2 2 ALA 3 3 ARG 4 4 GLY 5 5 TRP 6 6 GLY 7 7 ARG 8 8 LYS 9 9 CYS 10 10 PRO 11 11 LEU 12 12 PHE 13 13 GLY 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 . 32630 . . . . 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 mM Peptide VG13P, 0.1 mM TSP, 0.02 mM LPS, 55.5 M Water, 56.5 M D2O, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 1 mM 'natural abundance' LPS 0.02 mM 'natural abundance' TSP 0.1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % [U-2H] stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version 3.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AvanceIII _Field_strength 500 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_homonuclear_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D homonuclear TOCSY' _Sample_label $sample_1 save_ save_2D_trNOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D trNOESY' _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 4.5 0.1 pH pressure 1 . atm temperature 298 0.05 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 H 1 'methyl protons' ppm 0.000 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_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D homonuclear TOCSY' '2D trNOESY' 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 VAL HB H 2.028 0.007 1 2 1 1 VAL HG1 H 0.928 0.024 1 3 1 1 VAL HG2 H 0.928 0.024 1 4 2 2 ALA H H 8.354 0.024 1 5 2 2 ALA HA H 4.268 0.001 1 6 2 2 ALA HB H 1.335 0.007 1 7 3 3 ARG H H 8.213 0.002 1 8 3 3 ARG HA H 4.256 0.09 1 9 3 3 ARG HB2 H 1.711 0.004 1 10 3 3 ARG HB3 H 1.711 0.004 1 11 3 3 ARG HG2 H 1.579 0.001 1 12 3 3 ARG HG3 H 1.579 0.001 1 13 3 3 ARG HD2 H 3.138 0.006 1 14 3 3 ARG HD3 H 3.138 0.006 1 15 4 4 GLY H H 8.311 0.008 1 16 4 4 GLY HA2 H 3.857 0.018 1 17 4 4 GLY HA3 H 3.857 0.018 1 18 5 5 TRP H H 8.05 0.005 1 19 5 5 TRP HA H 4.666 0.002 1 20 5 5 TRP HB2 H 3.326 0.002 1 21 5 5 TRP HB3 H 3.335 0.002 1 22 5 5 TRP HD1 H 7.223 0.09 1 23 5 5 TRP HE3 H 7.584 0.001 1 24 5 5 TRP HZ3 H 7.137 0.007 1 25 6 6 GLY HA2 H 3.832 0.003 1 26 6 6 GLY HA3 H 3.832 0.003 1 27 7 7 ARG H H 8.015 0.003 1 28 7 7 ARG HA H 4.277 0.004 1 29 7 7 ARG HB2 H 1.81 0.002 1 30 7 7 ARG HB3 H 1.703 0.003 1 31 7 7 ARG HG2 H 1.587 0.001 1 32 7 7 ARG HG3 H 1.587 0.001 1 33 8 8 LYS H H 8.291 0.003 1 34 8 8 LYS HA H 4.341 0.002 1 35 8 8 LYS HB2 H 1.758 0.001 1 36 8 8 LYS HB3 H 1.758 0.001 1 37 8 8 LYS HG2 H 1.647 0.004 1 38 8 8 LYS HG3 H 1.647 0.004 1 39 8 8 LYS HD2 H 1.394 0.001 1 40 8 8 LYS HD3 H 1.394 0.001 1 41 9 9 CYS H H 8.43 0.002 1 42 9 9 CYS HA H 4.94 0.003 1 43 9 9 CYS HB2 H 3.21 0.002 1 44 9 9 CYS HB3 H 2.881 0.001 1 45 10 10 PRO HA H 4.35 0.001 1 46 10 10 PRO HB2 H 2.182 0.002 1 47 10 10 PRO HB3 H 2.182 0.002 1 48 10 10 PRO HG2 H 1.926 0.003 1 49 10 10 PRO HG3 H 1.926 0.003 1 50 10 10 PRO HD2 H 3.621 0.001 1 51 10 10 PRO HD3 H 3.621 0.001 1 52 11 11 LEU H H 8.14 0.001 1 53 11 11 LEU HA H 4.217 0.002 1 54 11 11 LEU HB2 H 1.502 0.001 1 55 11 11 LEU HB3 H 1.502 0.001 1 56 11 11 LEU HG H 1.407 0.002 1 57 11 11 LEU HD1 H 0.923 0.001 1 58 11 11 LEU HD2 H 0.923 0.001 1 59 12 12 PHE H H 8.145 0.001 1 60 12 12 PHE HA H 4.589 0.001 1 61 12 12 PHE HB2 H 3.125 0.001 1 62 12 12 PHE HB3 H 2.992 0.001 1 63 12 12 PHE HD1 H 7.22 0.001 1 64 12 12 PHE HD2 H 7.22 0.001 1 65 12 12 PHE HE1 H 7.334 0.001 1 66 12 12 PHE HE2 H 7.334 0.001 1 67 13 13 GLY HA2 H 3.819 0.001 1 68 13 13 GLY HA3 H 3.819 0.001 1 stop_ save_