data_36044 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure of gold nano particle-tagged VG16KRKP in Salmonella typhi LPS ; _BMRB_accession_number 36044 _BMRB_flat_file_name bmr36044.str _Entry_type original _Submission_date 2017-01-12 _Accession_date 2018-01-18 _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 Ilyas H. . . 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" 94 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2018-07-10 original BMRB . stop_ _Original_release_date 2018-01-18 save_ ############################# # Citation for this entry # ############################# save_citation_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Multivalent gold nanoparticle-peptide conjugates for targeting intracellular bacterial infections ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 28901372 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chowdhury R. . . 2 Ilyas H. . . 3 Ghosh A. . . 4 Ali H. . . 5 Ghorai A. . . 6 Midya A. . . 7 Jana N. R. . 8 Das S. . . 9 Bhunia A. . . stop_ _Journal_abbreviation Nanoscale _Journal_name_full Nanoscale _Journal_volume 9 _Journal_issue 37 _Journal_ISSN 2040-3372 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 14074 _Page_last 14093 _Year 2017 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name Au-VG16KRKP _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 Au-VG16KRKP _Molecular_mass 1765.157 _Mol_thiol_state 'all free' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 16 _Mol_residue_sequence ; VARGWKRKCPLFGKGG ; 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 LYS 7 7 ARG 8 8 LYS 9 9 CYS 10 10 PRO 11 11 LEU 12 12 PHE 13 13 GLY 14 14 LYS 15 15 GLY 16 16 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 'Dengue virus' 12637 Viruses . Flavivirus . 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 $entity_1 'chemical synthesis' . . . . . 'This sequence was chemically synthesized' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.5 mM None Au-VG16KRKP, 15 uM None LPS from S. typhosa, 55.5 M None H2O, 50 M None D2O, 1 mM None TSP, 90% H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.5 mM 'natural abundance' 'LPS from S. typhosa' 15 uM 'natural abundance' TSP 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 . loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task refinement 'structure calculation' stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 700 _Details 'with cryoprobe' 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' 0.00 0.00 M pH 6.5 0.00 pH pressure 1 0.00 atm temperature 298.15 0.00 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 TSP H 1 'methyl protons' ppm 0.00 external 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 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 $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 HA H 4.118 0.001 1 2 1 1 VAL HB H 1.564 0.001 1 3 1 1 VAL HG1 H 0.970 0.005 2 4 1 1 VAL HG2 H 0.970 0.005 2 5 2 2 ALA H H 8.431 0.001 1 6 2 2 ALA HA H 4.278 0.009 1 7 2 2 ALA HB H 1.415 0.006 1 8 3 3 ARG H H 8.222 0.016 1 9 3 3 ARG HA H 4.378 0.008 1 10 3 3 ARG HB2 H 1.912 0.0022 2 11 3 3 ARG HB3 H 1.815 0.005 2 12 3 3 ARG HG2 H 1.437 0.019 2 13 3 3 ARG HG3 H 1.437 0.019 2 14 3 3 ARG HD2 H 3.062 0.002 2 15 3 3 ARG HD3 H 3.062 0.002 2 16 4 4 GLY H H 8.317 0.003 1 17 4 4 GLY HA2 H 3.935 0.004 2 18 4 4 GLY HA3 H 3.935 0.004 2 19 5 5 TRP H H 7.990 0.002 1 20 5 5 TRP HA H 4.607 0.001 1 21 5 5 TRP HB2 H 3.271 0.001 2 22 5 5 TRP HB3 H 3.271 0.001 2 23 5 5 TRP HD1 H 7.272 0.006 1 24 5 5 TRP HE1 H 10.17 0.000 1 25 5 5 TRP HE3 H 7.575 0.001 1 26 5 5 TRP HZ2 H 7.505 0.002 1 27 5 5 TRP HZ3 H 7.150 0.000 1 28 5 5 TRP HH2 H 7.227 0.015 1 29 6 6 LYS H H 8.018 0.005 1 30 6 6 LYS HA H 4.149 0.000 1 31 6 6 LYS HB2 H 1.687 0.004 2 32 6 6 LYS HB3 H 1.687 0.004 2 33 6 6 LYS HG2 H 1.221 0.001 2 34 6 6 LYS HG3 H 1.221 0.001 2 35 6 6 LYS HD2 H 1.564 0.001 2 36 6 6 LYS HD3 H 1.564 0.001 2 37 7 7 ARG H H 8.522 0.224 1 38 7 7 ARG HA H 4.141 0.009 1 39 7 7 ARG HB2 H 1.700 0.001 2 40 7 7 ARG HB3 H 1.700 0.001 2 41 7 7 ARG HG2 H 1.580 0.002 2 42 7 7 ARG HG3 H 1.580 0.002 2 43 8 8 LYS H H 8.106 0.002 1 44 8 8 LYS HA H 4.141 0.009 1 45 8 8 LYS HB2 H 1.745 0.011 2 46 8 8 LYS HB3 H 1.745 0.011 2 47 8 8 LYS HG2 H 1.599 0.002 2 48 8 8 LYS HG3 H 1.599 0.002 2 49 8 8 LYS HE2 H 3.180 0.000 2 50 8 8 LYS HE3 H 3.180 0.000 2 51 9 9 CYS H H 8.367 0.007 1 52 9 9 CYS HA H 4.272 0.173 1 53 9 9 CYS HB2 H 2.917 0.005 1 54 9 9 CYS HB3 H 2.917 0.005 1 55 10 10 PRO HB2 H 2.230 0.083 1 56 10 10 PRO HB3 H 2.230 0.083 1 57 10 10 PRO HG2 H 1.988 0.002 2 58 10 10 PRO HG3 H 1.988 0.002 2 59 10 10 PRO HD2 H 3.768 0.001 1 60 10 10 PRO HD3 H 3.768 0.001 1 61 11 11 LEU H H 8.267 0.017 1 62 11 11 LEU HA H 4.250 0.802 1 63 11 11 LEU HB2 H 1.526 0.013 2 64 11 11 LEU HB3 H 1.526 0.013 2 65 11 11 LEU HG H 1.420 0.005 1 66 11 11 LEU HD1 H 0.872 0.004 2 67 11 11 LEU HD2 H 0.872 0.004 2 68 12 12 PHE H H 8.211 0.003 1 69 12 12 PHE HA H 4.601 0.006 1 70 12 12 PHE HB2 H 3.178 0.000 1 71 12 12 PHE HB3 H 3.178 0.000 1 72 12 12 PHE HD1 H 7.258 0.009 3 73 12 12 PHE HD2 H 7.258 0.009 3 74 12 12 PHE HE1 H 7.372 0.002 3 75 12 12 PHE HE2 H 7.372 0.002 3 76 13 13 GLY H H 8.311 0.008 1 77 13 13 GLY HA2 H 3.913 0.003 2 78 13 13 GLY HA3 H 3.913 0.003 2 79 14 14 LYS H H 8.211 0.006 1 80 14 14 LYS HA H 4.367 0.001 1 81 14 14 LYS HB2 H 1.802 0.004 2 82 14 14 LYS HB3 H 1.802 0.004 2 83 14 14 LYS HG2 H 1.451 0.001 2 84 14 14 LYS HG3 H 1.451 0.001 2 85 14 14 LYS HD2 H 1.705 0.000 2 86 14 14 LYS HD3 H 1.705 0.000 2 87 14 14 LYS HE2 H 3.088 0.000 2 88 14 14 LYS HE3 H 3.088 0.000 2 89 15 15 GLY H H 8.499 0.003 1 90 15 15 GLY HA2 H 3.972 0.000 2 91 15 15 GLY HA3 H 3.972 0.000 2 92 16 16 GLY H H 7.934 0.008 1 93 16 16 GLY HA2 H 3.768 0.001 2 94 16 16 GLY HA3 H 3.768 0.001 2 stop_ save_