data_20115 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Substance P 40 structures in water pH 5.5 298 K NMR DATA & STRUCTURES ; _BMRB_accession_number 20115 _BMRB_flat_file_name bmr20115.str _Entry_type new _Submission_date 2009-12-31 _Accession_date 2009-12-31 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'structures generated by XPLOR-NIH checked by PSVS server in water' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gayen Anindita . . 2 Mukhopadhyay Chaitali . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 structure_coordinate_set 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 82 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-03-17 update BMRB 'PDBj annotated the coordinate file' 2011-02-03 update BMRB 'update entry citation' 2010-10-27 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 20116 'Substance P in DMPC:CHAPS q=0.25 bicelles' 20117 'Substance P in isotropic q=0.25 DMPC/CHAPS/GM1 bicelles' 16660 'SUBSTANCE P IN WATER COMPLEXED WITH NK1R' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 20937248 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gayen Anindita . . 2 Goswami 'Sudipto Kishore' . . 3 Mukhopadhyay Chaitali . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_name_full 'Biochimica et biophysica acta' _Journal_volume 1808 _Journal_issue 1 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 127 _Page_last 139 _Year 2011 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Substance P' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'Substance P' $Substance_P stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . loop_ _Biological_function Neuromodulator stop_ _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Substance_P _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Substance_P _Molecular_mass . _Mol_thiol_state 'not present' loop_ _Biological_function Neuromodulator stop_ _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 11 _Mol_residue_sequence RPKPQQFFGLM loop_ _Residue_seq_code _Residue_label 1 ARG 2 PRO 3 LYS 4 PRO 5 GLN 6 GLN 7 PHE 8 PHE 9 GLY 10 LEU 11 MET 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 $Substance_P Human 9606 Eukaryota Metazoa Homo sapiens 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 $Substance_P 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $Substance_P 3.7 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name X-PLOR_NIH _Version . loop_ _Vendor _Address _Electronic_address 'Charles Schwieters' . . stop_ loop_ _Task 'structure solution' refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 500 _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 298 . K pH 5.5 . 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 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 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 $X-PLOR_NIH stop_ loop_ _Experiment_label '2D 1H-1H TOCSY' 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 'Substance P' _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 ARG HA H 4.068 . 1 2 1 1 ARG HB2 H 1.824 . 1 3 1 1 ARG HB3 H 1.824 . 1 4 1 1 ARG HD2 H 3.222 . 1 5 1 1 ARG HD3 H 3.222 . 1 6 1 1 ARG HG2 H 1.305 . 1 7 1 1 ARG HG3 H 1.305 . 1 8 2 2 PRO HA H 4.441 . 1 9 2 2 PRO HB2 H 1.865 . 2 10 2 2 PRO HB3 H 1.998 . 2 11 2 2 PRO HD2 H 3.592 . 2 12 2 2 PRO HD3 H 3.749 . 2 13 2 2 PRO HG2 H 1.839 . 2 14 2 2 PRO HG3 H 1.862 . 2 15 3 3 LYS H H 8.478 . 1 16 3 3 LYS HA H 4.452 . 1 17 3 3 LYS HB2 H 1.816 . 1 18 3 3 LYS HB3 H 1.816 . 1 19 3 3 LYS HD2 H 1.680 . 1 20 3 3 LYS HD3 H 1.680 . 1 21 3 3 LYS HE2 H 2.982 . 1 22 3 3 LYS HE3 H 2.982 . 1 23 3 3 LYS HG2 H 1.498 . 1 24 3 3 LYS HG3 H 1.498 . 1 25 4 4 PRO HA H 4.37 . 1 26 4 4 PRO HB2 H 1.993 . 2 27 4 4 PRO HB3 H 2.011 . 2 28 4 4 PRO HD2 H 3.632 . 2 29 4 4 PRO HD3 H 3.837 . 2 30 4 4 PRO HG2 H 1.868 . 2 31 4 4 PRO HG3 H 2.313 . 2 32 5 5 GLN H H 8.446 . 1 33 5 5 GLN HA H 4.193 . 1 34 5 5 GLN HB2 H 1.939 . 1 35 5 5 GLN HB3 H 1.939 . 1 36 5 5 GLN HE21 H 6.87 . 2 37 5 5 GLN HE22 H 7.516 . 2 38 5 5 GLN HG2 H 2.262 . 1 39 5 5 GLN HG3 H 2.262 . 1 40 6 6 GLN H H 8.244 . 1 41 6 6 GLN HA H 4.217 . 1 42 6 6 GLN HB2 H 1.810 . 1 43 6 6 GLN HB3 H 1.810 . 1 44 6 6 GLN HE21 H 6.857 . 2 45 6 6 GLN HE22 H 7.422 . 2 46 6 6 GLN HG2 H 2.128 . 1 47 6 6 GLN HG3 H 2.128 . 1 48 7 7 PHE H H 8.204 . 1 49 7 7 PHE HA H 4.571 . 1 50 7 7 PHE HB2 H 2.892 . 2 51 7 7 PHE HB3 H 3.045 . 2 52 7 7 PHE HD1 H 7.189 . 1 53 7 7 PHE HD2 H 7.189 . 1 54 7 7 PHE HE1 H 7.295 . 1 55 7 7 PHE HE2 H 7.295 . 1 56 7 7 PHE HZ H 7.255 . 1 57 8 8 PHE H H 8.198 . 1 58 8 8 PHE HA H 4.588 . 1 59 8 8 PHE HB2 H 2.920 . 2 60 8 8 PHE HB3 H 3.154 . 2 61 8 8 PHE HD1 H 7.246 . 1 62 8 8 PHE HD2 H 7.246 . 1 63 8 8 PHE HE1 H 7.336 . 1 64 8 8 PHE HE2 H 7.336 . 1 65 8 8 PHE HZ H 7.31 . 1 66 9 9 GLY H H 7.862 . 1 67 9 9 GLY HA2 H 3.852 . 1 68 9 9 GLY HA3 H 3.852 . 1 69 10 10 LEU H H 8.120 . 1 70 10 10 LEU HA H 4.315 . 1 71 10 10 LEU HB2 H 1.613 . 1 72 10 10 LEU HB3 H 1.613 . 1 73 10 10 LEU HD1 H 0.935 . 1 74 10 10 LEU HD2 H 0.887 . 1 75 10 10 LEU HG H 1.613 . 1 76 11 11 MET H H 8.329 . 1 77 11 11 MET HA H 4.445 . 1 78 11 11 MET HB2 H 2.005 . 2 79 11 11 MET HB3 H 2.070 . 2 80 11 11 MET HE H 7.096 . 1 81 11 11 MET HG2 H 2.490 . 2 82 11 11 MET HG3 H 2.605 . 2 stop_ save_