data_19932 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution NMR structure of peptide ImI1 (peak 2) ; _BMRB_accession_number 19932 _BMRB_flat_file_name bmr19932.str _Entry_type original _Submission_date 2014-04-24 _Accession_date 2014-04-24 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'Bicyclic peptide ImI1 (peak 2) was generated by substituing two adjacent cysteines in ImI with a dithiol amino acid 1a.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Heinis Christian . . 2 Chen Shiyu . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 63 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-09-22 original author . stop_ _Original_release_date 2014-09-22 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Synthetic di-thiol containing amino acids for structurally shaping polypeptides and enhancing target-ligand binding interactions' _Citation_status submitted _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 Chen Shiyu . . 2 Gopalakrishnan Ranganath . . 3 Schaer Tifany . . 4 Marger Fabrice . . 5 Hovius Ruud . . 6 Bertrand Daniel . . 7 Pojer Florence . . 8 Heinis Christian . . 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 'peptide ImI1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'peptide ImI1' $ImI1_(peak_2) 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_ImI1_(peak_2) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common ImI1_(peak_2) _Molecular_mass 1202.379 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 13 _Mol_residue_sequence GXASDPRCAWRCX loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 81S 3 3 ALA 4 4 SER 5 5 ASP 6 6 PRO 7 7 ARG 8 8 CYS 9 9 ALA 10 10 TRP 11 11 ARG 12 12 CYS 13 13 NH2 stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_81S _Saveframe_category polymer_residue _Mol_type 'L-PEPTIDE LINKING' _Name_common (4S)-4,5-disulfanyl-L-norvaline _BMRB_code 81S _PDB_code 81S _Standard_residue_derivative . _Molecular_mass 181.276 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CD1 CD1 C . 0 . ? SE SE S . 0 . ? SD2 SD2 S . 0 . ? C C C . 0 . ? O O O . 0 . ? H1 H1 H . 0 . ? H2 H2 H . 0 . ? H4 H4 H . 0 . ? H5 H5 H . 0 . ? H6 H6 H . 0 . ? H7 H7 H . 0 . ? H8 H8 H . 0 . ? H9 H9 H . 0 . ? H10 H10 H . 0 . ? H11 H11 H . 0 . ? OXT OXT O . 0 . ? H3 H3 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name DOUB O C ? ? SING C CA ? ? SING SD2 CG ? ? SING CG CB ? ? SING CG CD1 ? ? SING CB CA ? ? SING CA N ? ? SING CD1 SE ? ? SING N H1 ? ? SING N H2 ? ? SING CA H4 ? ? SING CB H5 ? ? SING CB H6 ? ? SING CG H7 ? ? SING CD1 H8 ? ? SING CD1 H9 ? ? SING SE H10 ? ? SING SD2 H11 ? ? SING C OXT ? ? SING OXT H3 ? ? stop_ save_ save_chem_comp_NH2 _Saveframe_category polymer_residue _Mol_type NON-POLYMER _Name_common 'AMINO GROUP' _BMRB_code NH2 _PDB_code NH2 _Standard_residue_derivative . _Molecular_mass 16.023 _Mol_paramagnetic . _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons N N N . 0 . ? HN1 HN1 H . 0 . ? HN2 HN2 H . 0 . ? stop_ loop_ _Bond_order _Bond_atom_one_atom_name _Bond_atom_two_atom_name _PDB_bond_atom_one_atom_name _PDB_bond_atom_two_atom_name SING N HN1 ? ? SING N HN2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $ImI1_(peak_2) . . . . . . 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 $ImI1_(peak_2) 'chemical synthesis' . . . . . 'The peptide was synthesized by solid phase peptide synthesis using Fmoc chemistry.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM peptide was dissolved in 600 micro liter 100 mM potassium phosphate pH 5.8 buffer.' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $ImI1_(peak_2) 1 mM 'natural abundance' 'potassium phosphate buffer' 100 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.113 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details 'Sparky - NMR Assignment and Integration Software' save_ save_CNS _Saveframe_category software _Name CNS _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_AMBER _Saveframe_category software _Name AMBER _Version 11 loop_ _Vendor _Address _Electronic_address 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ save_ProcheckNMR _Saveframe_category software _Name ProcheckNMR _Version . loop_ _Vendor _Address _Electronic_address 'Laskowski and MacArthur' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing 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_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details '0.1 M potassium phosphate pH 5.8 buffer with 10 % D2O' loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 0.1 . M pH 5.8 . pH pressure 1 . atm temperature 278 . 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 TMS H 1 'methyl protons' ppm 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_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $SPARKY stop_ loop_ _Experiment_label '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 'peptide ImI1' _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 2 2 81S H4 H 4.116 0.004 1 2 2 2 81S H5 H 2.131 0.005 1 3 2 2 81S H6 H 1.947 0.003 1 4 2 2 81S H7 H 2.861 0.002 1 5 2 2 81S H8 H 2.980 0.002 1 6 2 2 81S H9 H 2.399 0.001 1 7 3 3 ALA H H 8.474 0.000 1 8 3 3 ALA HA H 3.798 0.001 1 9 3 3 ALA HB H 1.125 0.001 1 10 4 4 SER H H 7.502 0.003 1 11 4 4 SER HA H 4.202 0.002 1 12 4 4 SER HB2 H 3.718 0.000 1 13 4 4 SER HB3 H 3.571 0.008 1 14 5 5 ASP H H 7.282 0.001 1 15 5 5 ASP HA H 4.662 0.000 1 16 5 5 ASP HB2 H 2.842 0.012 1 17 5 5 ASP HB3 H 2.391 0.002 1 18 6 6 PRO HA H 4.122 0.006 1 19 6 6 PRO HB2 H 2.124 0.003 1 20 6 6 PRO HB3 H 1.735 0.004 1 21 6 6 PRO HG2 H 1.781 0.016 1 22 6 6 PRO HG3 H 1.781 0.016 1 23 6 6 PRO HD2 H 3.794 0.002 1 24 6 6 PRO HD3 H 3.736 0.004 1 25 7 7 ARG H H 8.158 0.001 1 26 7 7 ARG HA H 3.967 0.005 1 27 7 7 ARG HB2 H 1.662 0.002 1 28 7 7 ARG HB3 H 1.526 0.002 1 29 7 7 ARG HG2 H 1.393 0.001 1 30 7 7 ARG HG3 H 1.393 0.001 1 31 7 7 ARG HD2 H 2.964 0.000 1 32 7 7 ARG HD3 H 2.910 0.002 1 33 7 7 ARG HE H 7.338 0.001 1 34 8 8 CYS H H 7.513 0.003 1 35 8 8 CYS HA H 4.103 0.009 1 36 8 8 CYS HB2 H 2.972 0.007 1 37 8 8 CYS HB3 H 2.851 0.009 1 38 9 9 ALA H H 7.805 0.001 1 39 9 9 ALA HA H 3.848 0.004 1 40 9 9 ALA HB H 1.025 0.002 1 41 10 10 TRP H H 7.454 0.000 1 42 10 10 TRP HA H 4.421 0.001 1 43 10 10 TRP HB2 H 3.115 0.002 1 44 10 10 TRP HB3 H 3.045 0.003 1 45 10 10 TRP HD1 H 7.014 0.001 1 46 10 10 TRP HE1 H 9.969 0.000 1 47 10 10 TRP HE3 H 7.279 0.004 1 48 10 10 TRP HZ2 H 7.223 0.000 1 49 10 10 TRP HZ3 H 6.880 0.002 1 50 10 10 TRP HH2 H 6.950 0.002 1 51 11 11 ARG H H 7.694 0.003 1 52 11 11 ARG HA H 3.898 0.001 1 53 11 11 ARG HB2 H 1.245 0.005 1 54 11 11 ARG HB3 H 1.245 0.005 1 55 11 11 ARG HG2 H 1.001 0.005 1 56 11 11 ARG HG3 H 0.891 0.001 1 57 11 11 ARG HD2 H 2.759 0.002 1 58 11 11 ARG HD3 H 2.759 0.002 1 59 11 11 ARG HE H 6.914 0.002 1 60 12 12 CYS H H 7.855 0.003 1 61 12 12 CYS HA H 4.210 0.002 1 62 12 12 CYS HB2 H 2.796 0.001 1 63 12 12 CYS HB3 H 2.493 0.002 1 stop_ save_