data_17426 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution structure of SFTI-OPN, a pro-angiogenic peptide with osteopontin sequence grafted into SFTI-1 cyclic framework ; _BMRB_accession_number 17426 _BMRB_flat_file_name bmr17426.str _Entry_type original _Submission_date 2011-01-24 _Accession_date 2011-01-24 _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 Chan 'Lai Yue' Y. . 2 Daly 'Norelle Lee' L. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 71 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2012-03-09 update BMRB 'update entry citation' 2011-11-03 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Engineering pro-angiogenic peptides using stable, disulfide-rich cyclic scaffolds.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 22039263 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Chan Lai Y. . 2 Gunasekera Sunithi . . 3 Henriques Sonia T. . 4 Worth Nathalie F. . 5 Le Sarah-Jane . . 6 Clark Richard J. . 7 Campbell Julie H. . 8 Craik David J. . 9 Daly Norelle L. . stop_ _Journal_abbreviation Blood _Journal_name_full Blood _Journal_volume 118 _Journal_issue 25 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 6709 _Page_last 6717 _Year 2011 _Details . loop_ _Keyword pro-angiogenesis osteopontin laminin MCoTI-II SFTI-1 grafting 'cyclic peptide' 'promoting blood vessels growth' 'wound healing' 'diabetic retinopathy' 'rheumatoid arthritis' 'cardiac ischemia' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name SFTI-OPN _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label SFTI-OPN $SFTI-OPN 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_SFTI-OPN _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common SFTI-OPN _Molecular_mass 1551.82 _Mol_thiol_state 'all disulfide bound' loop_ _Biological_function pro-angiogenic stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence GRCSVVYGLRCFPD loop_ _Residue_seq_code _Residue_label 1 GLY 2 ARG 3 CYS 4 SER 5 VAL 6 VAL 7 TYR 8 GLY 9 LEU 10 ARG 11 CYS 12 PHE 13 PRO 14 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . 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 SFTI-OPN 3 CYS SG SFTI-OPN 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 $SFTI-OPN . . . . . . 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 $SFTI-OPN 'chemical synthesis' . . . . . 'Solid phase peptide synthesis using Boc chemistry' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '1 mM of SFTI-OPN was dissolved in 90%H2O/10% D2O' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $SFTI-OPN 1 mM 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CNS _Saveframe_category software _Name CNS _Version 1.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 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_ 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 . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units temperature 290 . K pH 5.0 . pH 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 _Indirect_shift_ratio_citation_label _Correction_value_citation_label water H 1 protons ppm 4.75 internal direct . . . 1.000000000 $entry_citation $entry_citation 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' '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 SFTI-OPN _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 8.210 0.001 1 2 1 1 GLY HA2 H 3.633 0.01 2 3 1 1 GLY HA3 H 3.979 0.01 2 4 2 2 ARG H H 7.699 0.01 1 5 2 2 ARG HA H 4.208 0.01 1 6 2 2 ARG HB3 H 1.695 0.01 2 7 2 2 ARG HG3 H 1.376 0.003 2 8 2 2 ARG HD3 H 2.968 0.005 2 9 3 3 CYS H H 8.481 0.001 1 10 3 3 CYS HA H 5.071 0.004 1 11 3 3 CYS HB2 H 2.753 0.01 2 12 3 3 CYS HB3 H 2.847 0.01 2 13 4 4 SER H H 8.738 0.01 1 14 4 4 SER HA H 4.470 0.01 1 15 4 4 SER HB2 H 3.667 0.01 2 16 4 4 SER HB3 H 3.796 0.01 2 17 5 5 VAL H H 8.309 0.001 1 18 5 5 VAL HA H 4.121 0.003 1 19 5 5 VAL HB H 2.004 0.01 1 20 5 5 VAL HG1 H 0.661 0.01 2 21 5 5 VAL HG2 H 0.661 0.01 2 22 6 6 VAL H H 7.612 0.001 1 23 6 6 VAL HA H 3.607 0.005 1 24 6 6 VAL HB H 1.606 0.006 1 25 6 6 VAL HG1 H 0.411 0.003 2 26 6 6 VAL HG2 H 0.624 0.002 2 27 7 7 TYR H H 8.081 0.01 1 28 7 7 TYR HA H 4.371 0.01 1 29 7 7 TYR HB2 H 2.727 0.01 2 30 7 7 TYR HB3 H 2.965 0.01 2 31 7 7 TYR HD1 H 6.922 0.001 3 32 7 7 TYR HD2 H 6.922 0.001 3 33 7 7 TYR HE1 H 6.612 0.002 3 34 7 7 TYR HE2 H 6.612 0.002 3 35 8 8 GLY H H 7.614 0.01 1 36 8 8 GLY HA2 H 3.437 0.01 2 37 8 8 GLY HA3 H 3.886 0.01 2 38 9 9 LEU H H 7.879 0.01 1 39 9 9 LEU HA H 4.254 0.01 1 40 9 9 LEU HB2 H 1.311 0.01 2 41 9 9 LEU HB3 H 1.431 0.01 2 42 9 9 LEU HD1 H 0.647 0.01 2 43 9 9 LEU HD2 H 0.647 0.01 2 44 10 10 ARG H H 8.309 0.01 1 45 10 10 ARG HA H 4.114 0.01 1 46 10 10 ARG HB2 H 1.505 0.01 2 47 10 10 ARG HG2 H 1.201 0.003 2 48 10 10 ARG HG3 H 1.277 0.01 2 49 10 10 ARG HD2 H 2.917 0.002 2 50 10 10 ARG HD3 H 2.917 0.002 2 51 11 11 CYS H H 8.351 0.01 1 52 11 11 CYS HA H 4.809 0.003 1 53 11 11 CYS HB2 H 2.584 0.01 2 54 11 11 CYS HB3 H 2.718 0.01 2 55 12 12 PHE H H 8.543 0.01 1 56 12 12 PHE HA H 4.654 0.002 1 57 12 12 PHE HB2 H 2.813 0.01 2 58 12 12 PHE HB3 H 3.136 0.003 2 59 12 12 PHE HD1 H 7.095 0.001 3 60 12 12 PHE HD2 H 7.095 0.001 3 61 13 13 PRO HA H 4.185 0.003 1 62 13 13 PRO HB2 H 2.201 0.01 2 63 13 13 PRO HB3 H 1.780 0.01 2 64 13 13 PRO HG2 H 1.951 0.01 2 65 13 13 PRO HG3 H 1.862 0.01 2 66 13 13 PRO HD2 H 3.706 0.004 2 67 13 13 PRO HD3 H 3.788 0.01 2 68 14 14 ASP H H 7.898 0.01 1 69 14 14 ASP HA H 4.342 0.002 1 70 14 14 ASP HB2 H 2.659 0.01 2 71 14 14 ASP HB3 H 2.919 0.01 2 stop_ save_