data_19865 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; LASSO PEPTIDE BASED INTEGRIN INHIBITOR: MICROCIN J25 VARIANT WITH RGDF SUBSTITUTION OF GLY12-ILE13-GLY14-THR15 ; _BMRB_accession_number 19865 _BMRB_flat_file_name bmr19865.str _Entry_type original _Submission_date 2014-03-18 _Accession_date 2014-03-18 _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 Hegemann J. D. . 2 Zimmermann M. . . 3 Knappe T. A. . 4 Xie X. . . 5 Marahiel M. A. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 116 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-09-29 update BMRB 'update entry citation' 2014-06-30 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Rational improvement of the affinity and selectivity of integrin binding of grafted lasso peptides.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24949551 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hegemann Julian D. . 2 'De Simone' Mariarosaria . . 3 Zimmermann Marcel . . 4 Knappe Thomas A. . 5 Xie Xiulan . . 6 'Di Leva' 'Francesco Saverio' S. . 7 Marinelli Luciana . . 8 Novellino Ettore . . 9 Zahler Stefan . . 10 Kessler Horst . . 11 Marahiel Mohamed A. . stop_ _Journal_abbreviation 'J. Med. Chem.' _Journal_name_full 'Journal of medicinal chemistry' _Journal_volume 57 _Journal_issue 13 _Journal_ISSN 1520-4804 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 5829 _Page_last 5834 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'LASSO PEPTIDE BASED INTEGRIN INHIBITOR: MICROCIN J25 VARIANT WITH RGDF SUBSTITUTION OF GLY12-ILE13-GLY14-THR15' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label MCCJ25(RGDF) $MCCJ25(RGDF) 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_MCCJ25(RGDF) _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common MCCJ25(RGDF) _Molecular_mass 2274.514 _Mol_thiol_state 'not present' _Details 'MCCJ25 HOMOLOGUE, WITH RGDF AT POSITIONS 12-15' ############################## # Polymer residue sequence # ############################## _Residue_count 21 _Mol_residue_sequence ; GGAGHVPEYFVRGDFPISFY G ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 GLY 3 3 ALA 4 4 GLY 5 5 HIS 6 6 VAL 7 7 PRO 8 8 GLU 9 9 TYR 10 10 PHE 11 11 VAL 12 12 ARG 13 13 GLY 14 14 ASP 15 15 PHE 16 16 PRO 17 17 ILE 18 18 SER 19 19 PHE 20 20 TYR 21 21 GLY stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-09 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 2MMT "Lasso Peptide-based Integrin Inhibitor: Microcin J25 Variant With Rgdf Substitution Of Gly12-ile13-gly14-thr15" 100.00 21 100.00 100.00 5.51e-05 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $MCCJ25(RGDF) 'E. coli' 562 Bacteria . Escherichia coli 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 $MCCJ25(RGDF) 'chemical synthesis' . . . . . 'PRODUCTION DEPENDENT ON PRESENCE OF PTUC202 PLASMID CONTAINING THE G12R I13G G14D T15F MUTATION WITHIN THE MICROCIN J25 PRECURSOR GENE MCJA.' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '12.6 mM MCCJ25(RGDF)' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $MCCJ25(RGDF) 12.6 mM 'natural abundance' methanol 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CYANA_2.1 _Saveframe_category software _Name CYANA_2.1 _Version . loop_ _Vendor _Address _Electronic_address 'GUNTERT, MUMENTHALER' . . stop_ loop_ _Task refinement 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_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _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_1H-1H_NOESY_3 _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 pH 7.0 . pH pressure 1.0 . atm temperature 298 . 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 DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 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 DQF-COSY' 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 MCCJ25(RGDF) _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 HA2 H 4.229 0.005 2 2 1 1 GLY HA3 H 3.544 0.003 2 3 1 1 GLY H H 7.952 0.003 1 4 2 2 GLY H H 9.027 0.002 1 5 2 2 GLY HA2 H 3.874 0.004 2 6 2 2 GLY HA3 H 4.210 0.001 2 7 3 3 ALA H H 8.543 0.001 1 8 3 3 ALA HA H 4.655 0.002 1 9 3 3 ALA HB H 1.308 0.002 1 10 4 4 GLY H H 7.776 0.002 1 11 4 4 GLY HA2 H 4.057 0.005 2 12 4 4 GLY HA3 H 3.495 0.001 2 13 5 5 HIS H H 7.364 0.004 1 14 5 5 HIS HA H 4.703 0.000 1 15 5 5 HIS HB2 H 2.920 0.001 1 16 5 5 HIS HB3 H 3.259 0.000 1 17 5 5 HIS HD2 H 7.369 0.000 1 18 5 5 HIS HE1 H 8.711 0.000 1 19 6 6 VAL H H 8.702 0.004 1 20 6 6 VAL HA H 4.686 0.005 1 21 6 6 VAL HB H 1.747 0.004 1 22 6 6 VAL HG1 H 1.080 0.030 2 23 6 6 VAL HG2 H 0.848 0.001 2 24 7 7 PRO HA H 4.238 0.003 1 25 7 7 PRO HB2 H 1.613 0.009 1 26 7 7 PRO HB3 H 1.807 0.001 1 27 7 7 PRO HG2 H 1.965 0.004 1 28 7 7 PRO HG3 H 2.200 0.004 1 29 7 7 PRO HD2 H 3.796 0.000 1 30 7 7 PRO HD3 H 4.130 0.000 1 31 8 8 GLU H H 8.288 0.002 1 32 8 8 GLU HA H 4.347 0.005 1 33 8 8 GLU HB2 H 1.652 0.004 1 34 8 8 GLU HB3 H 1.763 0.004 1 35 8 8 GLU HG2 H 1.858 0.005 1 36 8 8 GLU HG3 H 2.002 0.004 1 37 9 9 TYR H H 7.476 0.004 1 38 9 9 TYR HA H 4.498 0.003 1 39 9 9 TYR HB2 H 2.675 0.028 1 40 9 9 TYR HB3 H 2.908 0.005 1 41 9 9 TYR HD1 H 6.925 0.001 3 42 9 9 TYR HD2 H 6.925 0.001 3 43 9 9 TYR HE1 H 6.618 0.000 3 44 9 9 TYR HE2 H 6.618 0.000 3 45 10 10 PHE H H 8.093 0.002 1 46 10 10 PHE HA H 4.795 0.008 1 47 10 10 PHE HB2 H 2.764 0.003 1 48 10 10 PHE HB3 H 2.941 0.006 1 49 10 10 PHE HD1 H 7.020 0.054 3 50 10 10 PHE HD2 H 7.020 0.054 3 51 10 10 PHE HE1 H 7.150 0.000 3 52 10 10 PHE HE2 H 7.150 0.000 3 53 11 11 VAL H H 8.218 0.007 1 54 11 11 VAL HA H 4.237 0.004 1 55 11 11 VAL HB H 2.082 0.007 1 56 11 11 VAL HG1 H 0.940 0.028 2 57 11 11 VAL HG2 H 0.940 0.028 2 58 12 12 ARG H H 8.360 0.003 1 59 12 12 ARG HA H 4.143 0.009 1 60 12 12 ARG HB2 H 1.803 0.002 1 61 12 12 ARG HB3 H 1.890 0.012 1 62 12 12 ARG HG2 H 1.625 0.006 1 63 12 12 ARG HG3 H 1.662 0.013 1 64 12 12 ARG HD2 H 3.202 0.001 2 65 12 12 ARG HD3 H 3.202 0.001 2 66 12 12 ARG HE H 7.411 0.003 1 67 13 13 GLY H H 8.491 0.002 1 68 13 13 GLY HA2 H 3.525 0.018 2 69 13 13 GLY HA3 H 4.071 0.004 2 70 14 14 ASP H H 8.254 0.003 1 71 14 14 ASP HA H 4.663 0.003 1 72 14 14 ASP HB2 H 2.629 0.033 1 73 14 14 ASP HB3 H 2.751 0.003 1 74 15 15 PHE H H 8.212 0.002 1 75 15 15 PHE HA H 4.930 0.000 1 76 15 15 PHE HB2 H 2.971 0.007 1 77 15 15 PHE HB3 H 3.203 0.003 1 78 15 15 PHE HD1 H 7.300 0.000 3 79 15 15 PHE HD2 H 7.300 0.000 3 80 16 16 PRO HA H 4.449 0.007 1 81 16 16 PRO HB2 H 1.748 0.003 1 82 16 16 PRO HB3 H 1.891 0.000 1 83 16 16 PRO HG2 H 1.957 0.005 1 84 16 16 PRO HG3 H 2.071 0.006 1 85 16 16 PRO HD2 H 3.604 0.098 1 86 16 16 PRO HD3 H 3.870 0.004 1 87 17 17 ILE H H 7.820 0.003 1 88 17 17 ILE HA H 4.388 0.006 1 89 17 17 ILE HB H 1.870 0.003 1 90 17 17 ILE HG12 H 1.454 0.006 2 91 17 17 ILE HG13 H 1.454 0.006 2 92 17 17 ILE HG2 H 0.877 0.002 1 93 17 17 ILE HD1 H 1.121 0.005 1 94 18 18 SER H H 7.415 0.003 1 95 18 18 SER HA H 4.404 0.003 1 96 18 18 SER HB2 H 3.861 0.004 1 97 18 18 SER HB3 H 4.050 0.004 1 98 19 19 PHE H H 8.832 0.003 1 99 19 19 PHE HA H 5.442 0.004 1 100 19 19 PHE HB2 H 2.582 0.011 1 101 19 19 PHE HB3 H 2.540 0.011 1 102 19 19 PHE HD1 H 6.863 0.002 3 103 19 19 PHE HD2 H 6.863 0.002 3 104 19 19 PHE HE1 H 7.064 0.000 3 105 19 19 PHE HE2 H 7.064 0.000 3 106 20 20 TYR H H 9.509 0.002 1 107 20 20 TYR HA H 4.935 0.005 1 108 20 20 TYR HB2 H 3.024 0.018 1 109 20 20 TYR HB3 H 2.985 0.020 1 110 20 20 TYR HD1 H 6.966 0.003 3 111 20 20 TYR HD2 H 6.966 0.003 3 112 20 20 TYR HE1 H 6.719 0.000 3 113 20 20 TYR HE2 H 6.719 0.000 3 114 21 21 GLY H H 8.623 0.001 1 115 21 21 GLY HA2 H 3.855 0.000 2 116 21 21 GLY HA3 H 3.855 0.000 2 stop_ save_