data_20081 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; solution structures of bradykinin - penta-O-galloyl-D-glucopyranose complexe ; _BMRB_accession_number 20081 _BMRB_flat_file_name bmr20081.str _Entry_type new _Submission_date 2009-04-28 _Accession_date 2009-04-28 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'replacement of PDB structure 1JJQ because it contained some chirality errors for the sugar PGG (Penta Galloyl Glucose).I asked PDB to erase the entry 1JJQ.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Monti Jean-Pierre . . 2 Verge Sarah . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 57 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2011-02-15 update BMRB 'PDBj annotated the coordinate file' 2010-04-15 update BMRB 'add related PDB ID' 2009-06-11 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'First observation of solution structures of bradykinin-penta-O-galloyl-D-glucopyranose complexes as determined by NMR and simulated annealing.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 12049789 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Verge Sarah . . 2 Richard Tristan . . 3 Moreau Serge . . 4 Nurich Alain . . 5 Merillon Jean-Michel . . 6 Vercauteren Joseph . . 7 Monti Jean-Pierre . . stop_ _Journal_abbreviation 'Biochim. Biophys. Acta' _Journal_volume 1571 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 89 _Page_last 101 _Year 2002 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'complex BK-PGG' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label bradykinin $bradykinin penta-O-galloyl-D-glucopyranose $GGP stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details 'complex between one polyphenol molecule (PGG) and one peptide (bradykinin-BK)' save_ ######################## # Monomeric polymers # ######################## save_bradykinin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common bradykinin _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 9 _Mol_residue_sequence RPPGFSPFR loop_ _Residue_seq_code _Residue_label 1 ARG 2 PRO 3 PRO 4 GLY 5 PHE 6 SER 7 PRO 8 PHE 9 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ############# # Ligands # ############# save_GGP _Saveframe_category ligand _Mol_type non-polymer _Name_common "GGP (BETA-1,2,3,4,6-PENTA-O-GALLOYL-D-GLUCOPYRANOSE)" _BMRB_code . _PDB_code GGP _Molecular_mass 940.677 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic yes _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Tue Nov 18 19:15:17 2008 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? O6 O6 O . 0 . ? O7 O7 O . 0 . ? C8 C8 C . 0 . ? O9 O9 O . 0 . ? C10 C10 C . 0 . ? C11 C11 C . 0 . ? C12 C12 C . 0 . ? O13 O13 O . 0 . ? C14 C14 C . 0 . ? O15 O15 O . 0 . ? C16 C16 C . 0 . ? O17 O17 O . 0 . ? C18 C18 C . 0 . ? C19 C19 C . 0 . ? O20 O20 O . 0 . ? C21 C21 C . 0 . ? C22 C22 C . 0 . ? C23 C23 C . 0 . ? O24 O24 O . 0 . ? C25 C25 C . 0 . ? O26 O26 O . 0 . ? C27 C27 C . 0 . ? O28 O28 O . 0 . ? C29 C29 C . 0 . ? C30 C30 C . 0 . ? O31 O31 O . 0 . ? O32 O32 O . 0 . ? C33 C33 C . 0 . ? O34 O34 O . 0 . ? C35 C35 C . 0 . ? C36 C36 C . 0 . ? C37 C37 C . 0 . ? O38 O38 O . 0 . ? C39 C39 C . 0 . ? O40 O40 O . 0 . ? C41 C41 C . 0 . ? O42 O42 O . 0 . ? C43 C43 C . 0 . ? O44 O44 O . 0 . ? C45 C45 C . 0 . ? O46 O46 O . 0 . ? C47 C47 C . 0 . ? C48 C48 C . 0 . ? C49 C49 C . 0 . ? O50 O50 O . 0 . ? C51 C51 C . 0 . ? O52 O52 O . 0 . ? C53 C53 C . 0 . ? O54 O54 O . 0 . ? C55 C55 C . 0 . ? O56 O56 O . 0 . ? C57 C57 C . 0 . ? O58 O58 O . 0 . ? C59 C59 C . 0 . ? C60 C60 C . 0 . ? C61 C61 C . 0 . ? O62 O62 O . 0 . ? C63 C63 C . 0 . ? O64 O64 O . 0 . ? C65 C65 C . 0 . ? O66 O66 O . 0 . ? C67 C67 C . 0 . ? HC1 HC1 H . 0 . ? HC2 HC2 H . 0 . ? HC3 HC3 H . 0 . ? HC4 HC4 H . 0 . ? HC5 HC5 H . 0 . ? H11 H11 H . 0 . ? H13 H13 H . 0 . ? H15 H15 H . 0 . ? H17 H17 H . 0 . ? H18 H18 H . 0 . ? H22 H22 H . 0 . ? H24 H24 H . 0 . ? H26 H26 H . 0 . ? H28 H28 H . 0 . ? H29 H29 H . 0 . ? H301 H301 H . 0 . ? H302 H302 H . 0 . ? H36 H36 H . 0 . ? H38 H38 H . 0 . ? H40 H40 H . 0 . ? H42 H42 H . 0 . ? H43 H43 H . 0 . ? H48 H48 H . 0 . ? H50 H50 H . 0 . ? H52 H52 H . 0 . ? H54 H54 H . 0 . ? H55 H55 H . 0 . ? H60 H60 H . 0 . ? H62 H62 H . 0 . ? H64 H64 H . 0 . ? H66 H66 H . 0 . ? H67 H67 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 C1 C2 ? ? SING C1 O6 ? ? SING C1 C30 ? ? SING C1 HC1 ? ? SING C2 C3 ? ? SING C2 O32 ? ? SING C2 HC2 ? ? SING C3 C4 ? ? SING C3 O56 ? ? SING C3 HC3 ? ? SING C4 C5 ? ? SING C4 O44 ? ? SING C4 HC4 ? ? SING C5 O6 ? ? SING C5 O7 ? ? SING C5 HC5 ? ? SING O7 C8 ? ? DOUB C8 O9 ? ? SING C8 C10 ? ? SING C10 C11 ? ? DOUB C10 C18 ? ? DOUB C11 C12 ? ? SING C11 H11 ? ? SING C12 O13 ? ? SING C12 C14 ? ? SING O13 H13 ? ? SING C14 O15 ? ? DOUB C14 C16 ? ? SING O15 H15 ? ? SING C16 O17 ? ? SING C16 C18 ? ? SING O17 H17 ? ? SING C18 H18 ? ? DOUB C19 O20 ? ? SING C19 C21 ? ? SING C19 O31 ? ? DOUB C21 C22 ? ? SING C21 C29 ? ? SING C22 C23 ? ? SING C22 H22 ? ? SING C23 O24 ? ? DOUB C23 C25 ? ? SING O24 H24 ? ? SING C25 O26 ? ? SING C25 C27 ? ? SING O26 H26 ? ? SING C27 O28 ? ? DOUB C27 C29 ? ? SING O28 H28 ? ? SING C29 H29 ? ? SING C30 O31 ? ? SING C30 H301 ? ? SING C30 H302 ? ? SING O32 C33 ? ? DOUB C33 O34 ? ? SING C33 C35 ? ? DOUB C35 C36 ? ? SING C35 C43 ? ? SING C36 C37 ? ? SING C36 H36 ? ? SING C37 O38 ? ? DOUB C37 C39 ? ? SING O38 H38 ? ? SING C39 O40 ? ? SING C39 C41 ? ? SING O40 H40 ? ? SING C41 O42 ? ? DOUB C41 C43 ? ? SING O42 H42 ? ? SING C43 H43 ? ? SING O44 C45 ? ? DOUB C45 O46 ? ? SING C45 C47 ? ? DOUB C47 C48 ? ? SING C47 C55 ? ? SING C48 C49 ? ? SING C48 H48 ? ? SING C49 O50 ? ? DOUB C49 C51 ? ? SING O50 H50 ? ? SING C51 O52 ? ? SING C51 C53 ? ? SING O52 H52 ? ? SING C53 O54 ? ? DOUB C53 C55 ? ? SING O54 H54 ? ? SING C55 H55 ? ? SING O56 C57 ? ? DOUB C57 O58 ? ? SING C57 C59 ? ? DOUB C59 C60 ? ? SING C59 C67 ? ? SING C60 C61 ? ? SING C60 H60 ? ? SING C61 O62 ? ? DOUB C61 C63 ? ? SING O62 H62 ? ? SING C63 O64 ? ? SING C63 C65 ? ? SING O64 H64 ? ? SING C65 O66 ? ? DOUB C65 C67 ? ? SING O66 H66 ? ? SING C67 H67 ? ? stop_ _Mol_thiol_state . _Sequence_homology_query_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $bradykinin 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 $bradykinin '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 $bradykinin 20 mM 'natural abundance' $GGP 20 mM 'natural abundance' H2O 90 % 'natural abundance' DMSO 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_InsightII _Saveframe_category software _Name InsightII _Version . loop_ _Vendor _Address _Electronic_address 'Accelrys Software Inc.' . . stop_ loop_ _Task 'geometry optimization' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _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_ROESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ROESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HMBC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HMBC' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _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 303 1 K pH 6.4 0.1 pH pressure 1 . atm 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_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-1H ROESY' 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 bradykinin _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 4.38 0.003 1 2 1 1 ARG HB2 H 1.97 0.005 1 3 1 1 ARG HB3 H 1.97 0.005 1 4 1 1 ARG HD2 H 3.33 0.003 1 5 1 1 ARG HD3 H 3.33 0.003 1 6 1 1 ARG HG2 H 1.77 0.003 1 7 1 1 ARG HG3 H 1.77 0.003 1 8 2 2 PRO HA H 4.77 0.005 1 9 2 2 PRO HB2 H 2.40 0.006 2 10 2 2 PRO HB3 H 1.91 0.006 2 11 2 2 PRO HD2 H 3.75 0.004 2 12 2 2 PRO HD3 H 3.51 0.003 2 13 2 2 PRO HG2 H 2.02 0.005 1 14 2 2 PRO HG3 H 2.02 0.005 1 15 3 3 PRO HA H 4.49 0.002 1 16 3 3 PRO HB2 H 2.34 0.003 2 17 3 3 PRO HB3 H 1.97 0.004 2 18 3 3 PRO HD2 H 3.84 0.002 2 19 3 3 PRO HD3 H 3.68 0.005 2 20 3 3 PRO HG2 H 2.10 0.004 1 21 3 3 PRO HG3 H 2.10 0.004 1 22 4 4 GLY H H 8.37 0.002 1 23 4 4 GLY HA2 H 3.98 0.006 1 24 4 4 GLY HA3 H 3.98 0.006 1 25 5 5 PHE H H 8.06 0.003 1 26 5 5 PHE HA H 4.65 0.004 1 27 5 5 PHE HB2 H 3.08 0.003 1 28 5 5 PHE HB3 H 3.08 0.003 1 29 5 5 PHE HD2 H 7.22 0.005 3 30 5 5 PHE HE2 H 7.31 0.003 3 31 5 5 PHE HZ H 7.28 0.004 1 32 6 6 SER H H 8.16 0.003 1 33 6 6 SER HA H 4.73 0.005 1 34 6 6 SER HB2 H 3.83 0.003 1 35 6 6 SER HB3 H 3.83 0.003 1 36 7 7 PRO HA H 4.40 0.003 1 37 7 7 PRO HB2 H 2.16 0.003 2 38 7 7 PRO HB3 H 1.67 0.003 2 39 7 7 PRO HD2 H 3.60 0.005 1 40 7 7 PRO HD3 H 3.60 0.005 1 41 7 7 PRO HG2 H 1.87 0.003 1 42 7 7 PRO HG3 H 1.87 0.003 1 43 8 8 PHE H H 7.96 0.004 1 44 8 8 PHE HA H 4.69 0.004 1 45 8 8 PHE HB2 H 3.27 0.006 2 46 8 8 PHE HB3 H 3.00 0.003 2 47 8 8 PHE HD2 H 7.27 0.005 3 48 8 8 PHE HE2 H 7.35 0.003 3 49 8 8 PHE HZ H 7.30 0.002 1 50 9 9 ARG H H 7.76 0.003 1 51 9 9 ARG HA H 4.26 0.003 1 52 9 9 ARG HB2 H 1.91 0.006 2 53 9 9 ARG HB3 H 1.78 0.006 2 54 9 9 ARG HD2 H 3.23 0.004 1 55 9 9 ARG HD3 H 3.23 0.004 1 56 9 9 ARG HG2 H 1.62 0.004 1 57 9 9 ARG HG3 H 1.62 0.004 1 stop_ save_