data_15122 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Structure and dynamics of surfactin studied by NMR in micellar media ; _BMRB_accession_number 15122 _BMRB_flat_file_name bmr15122.str _Entry_type original _Submission_date 2007-01-31 _Accession_date 2007-01-31 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'surfactin in SDS micellar aqueous solution' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tsan P. . . 2 Volpon L. . . 3 Lancelin J. M. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 2 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 57 "15N chemical shifts" 7 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-03-06 original author . stop_ _Original_release_date 2007-03-06 save_ ############################# # Citation for this entry # ############################# save_citations _Saveframe_category entry_citation _Citation_full . _Citation_title 'Structure and dynamics of surfactin studied by NMR in micellar media' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 17256853 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Tsan P. . . 2 Volpon L. . . 3 Besson F. . . 4 Lancelin J. M. . stop_ _Journal_abbreviation 'J. Am. Chem. Soc.' _Journal_name_full 'Journal of the American Chemistry Society' _Journal_volume 129 _Journal_issue 7 _Journal_CSD 0353 _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1968 _Page_last 1977 _Year 2007 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name surfactin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label surfactin $surfactin (R)-3-HYDROXYTETRADECANAL $entity_BFC 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_surfactin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common ELLVDLL _Molecular_mass . _Mol_thiol_state 'not present' _Details ; This biosurfactant is a cyclic lipopeptide with seven amino-acids (Glu-Leu-Leu-Val-Asp-Leu-Leu) of configuration LLDLLDL and one beta-amino fatty acid. ; ############################## # Polymer residue sequence # ############################## _Residue_count 7 _Mol_residue_sequence ELXVDXL loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 2 GLU 2 3 LEU 3 4 DLE 4 5 VAL 5 6 ASP 6 7 DLE 7 8 LEU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DLE _Saveframe_category polymer_residue _Mol_type 'D-PEPTIDE LINKING' _Name_common D-LEUCINE _BMRB_code DLE _PDB_code DLE _Standard_residue_derivative . _Molecular_mass 131.173 _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 . ? CD2 CD2 C . 0 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG H . 0 . ? HD11 HD11 H . 0 . ? HD12 HD12 H . 0 . ? HD13 HD13 H . 0 . ? HD21 HD21 H . 0 . ? HD22 HD22 H . 0 . ? HD23 HD23 H . 0 . ? HXT HXT 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 CA ? ? SING N H ? ? SING N H2 ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB CG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING CG CD1 ? ? SING CG CD2 ? ? SING CG HG ? ? SING CD1 HD11 ? ? SING CD1 HD12 ? ? SING CD1 HD13 ? ? SING CD2 HD21 ? ? SING CD2 HD22 ? ? SING CD2 HD23 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ ############# # Ligands # ############# save_BFC _Saveframe_category ligand _Mol_type "non-polymer (NON-POLYMER)" _Name_common (R)-3-HYDROXYTETRADECANAL _BMRB_code BFC _PDB_code BFC _Molecular_mass 228.371 _Mol_charge 0 _Mol_paramagnetic . _Mol_aromatic no _Details . loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? O O O . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? OB OB O . 0 . ? CC CC C . 0 . ? CD CD C . 0 . ? CE CE C . 0 . ? CF CF C . 0 . ? CG CG C . 0 . ? CH CH C . 0 . ? CI CI C . 0 . ? CJ CJ C . 0 . ? CK CK C . 0 . ? CL CL C . 0 . ? CM CM C . 0 . ? H H H . 0 . ? HA1 HA1 H . 0 . ? HA2 HA2 H . 0 . ? HB HB H . 0 . ? HOB HOB H . 0 . ? HC1 HC1 H . 0 . ? HC2 HC2 H . 0 . ? HD1 HD1 H . 0 . ? HD2 HD2 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 H . 0 . ? HF1 HF1 H . 0 . ? HF2 HF2 H . 0 . ? HG1 HG1 H . 0 . ? HG2 HG2 H . 0 . ? HH1 HH1 H . 0 . ? HH2 HH2 H . 0 . ? HI1 HI1 H . 0 . ? HI2 HI2 H . 0 . ? HJ1 HJ1 H . 0 . ? HJ2 HJ2 H . 0 . ? HK1 HK1 H . 0 . ? HK2 HK2 H . 0 . ? HL1 HL1 H . 0 . ? HL2 HL2 H . 0 . ? HM1 HM1 H . 0 . ? HM2 HM2 H . 0 . ? HM3 HM3 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 C CA ? ? DOUB C O ? ? SING C H ? ? SING CA CB ? ? SING CA HA1 ? ? SING CA HA2 ? ? SING CB OB ? ? SING CB CC ? ? SING CB HB ? ? SING OB HOB ? ? SING CC CD ? ? SING CC HC1 ? ? SING CC HC2 ? ? SING CD CE ? ? SING CD HD1 ? ? SING CD HD2 ? ? SING CE CF ? ? SING CE HE1 ? ? SING CE HE2 ? ? SING CF CG ? ? SING CF HF1 ? ? SING CF HF2 ? ? SING CG CH ? ? SING CG HG1 ? ? SING CG HG2 ? ? SING CH CI ? ? SING CH HH1 ? ? SING CH HH2 ? ? SING CI CJ ? ? SING CI HI1 ? ? SING CI HI2 ? ? SING CJ CK ? ? SING CJ HJ1 ? ? SING CJ HJ2 ? ? SING CK CL ? ? SING CK HK1 ? ? SING CK HK2 ? ? SING CL CM ? ? SING CL HL1 ? ? SING CL HL2 ? ? SING CM HM1 ? ? SING CM HM2 ? ? SING CM HM3 ? ? 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 _Details $surfactin bacteria . . . Bacillus subtilis ; This peptide that contained amino acids with configuration d was purified from bacteria. For such peptides, the bacteria are using multienzymatic systems that racemize amino acid and catalyze the formation of peptidic bond, as for the synthesis of peptidoglycans for example. ; 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 $surfactin 'purified from the natural source' . bacillus subtilis . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample _Saveframe_category sample _Sample_type solution _Details '4mM surfactin in 90% H2O, 10% D2O (pH 5.1); 50mM SDS-d25' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $surfactin 4 mM [U-15N] SDS 50 mM '[U-99% 2H]' stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version . loop_ _Vendor _Address _Electronic_address 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' . . stop_ loop_ _Task processing stop_ _Details . save_ save_GIFA _Saveframe_category software _Name GIFA _Version 4.0 loop_ _Vendor _Address _Electronic_address 'Marc-Andre Delsuc' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_Molmol _Saveframe_category software _Name Molmol _Version . loop_ _Vendor _Address _Electronic_address 'Koradi, Billeter and Wuthrich' . . stop_ loop_ _Task 'data analysis' stop_ _Details . save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version . loop_ _Vendor _Address _Electronic_address Brunger . . stop_ loop_ _Task 'structure solution' 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_DQF-COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample save_ save_2D_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample save_ save_2D_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample save_ save_2D_1H-15N_HSQC_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $sample save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.1 . pH pressure 1 . 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 H 1 'methyl protons' ppm 0 internal direct . . . 1 DSS N 15 'methyl protons' ppm 0 . 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_2 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label DQF-COSY '2D TOCSY' '2D NOESY' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name (R)-3-HYDROXYTETRADECANAL _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 BFC H H 8.14 0.02 1 2 1 1 BFC HA1 H 2.32 0.02 2 3 1 1 BFC HA2 H 2.81 0.02 2 4 1 1 BFC HB H 5.05 0.02 1 5 1 1 BFC HG1 H 1.62 0.02 2 6 1 1 BFC HG2 H 1.85 0.02 2 stop_ save_ save_assigned_chem_shift_list_1_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label DQF-COSY '2D TOCSY' '2D NOESY' '2D 1H-15N HSQC' stop_ loop_ _Sample_label $sample stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name surfactin _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 1 GLU H H 8.19 0.02 1 2 2 1 GLU HA H 4.29 0.02 1 3 2 1 GLU HB2 H 1.76 0.02 2 4 2 1 GLU HB3 H 1.85 0.02 2 5 2 1 GLU HG2 H 2.08 0.02 2 6 2 1 GLU HG3 H 2.16 0.02 2 7 2 1 GLU N N 128.9 0.2 1 8 3 2 LEU H H 7.90 0.02 1 9 3 2 LEU HA H 4.19 0.02 1 10 3 2 LEU HB2 H 1.51 0.02 2 11 3 2 LEU HB3 H 1.62 0.02 2 12 3 2 LEU HG H 1.65 0.02 1 13 3 2 LEU HD1 H 0.90 0.02 2 14 3 2 LEU HD2 H 0.92 0.02 2 15 3 2 LEU N N 122.8 0.2 1 16 4 3 DLE N N 123.9 0.2 1 17 4 3 DLE H H 8.14 0.02 1 18 4 3 DLE HA H 4.40 0.02 1 19 4 3 DLE HB2 H 1.57 0.02 2 20 4 3 DLE HB3 H 1.67 0.02 2 21 4 3 DLE HG H 1.73 0.02 1 22 4 3 DLE HD11 H 0.86 0.02 2 23 4 3 DLE HD12 H 0.86 0.02 2 24 4 3 DLE HD13 H 0.86 0.02 2 25 4 3 DLE HD21 H 0.92 0.02 2 26 4 3 DLE HD22 H 0.92 0.02 2 27 4 3 DLE HD23 H 0.92 0.02 2 28 5 4 VAL H H 8.09 0.02 1 29 5 4 VAL HA H 3.90 0.02 1 30 5 4 VAL HB H 1.99 0.02 1 31 5 4 VAL HG1 H 0.78 0.02 2 32 5 4 VAL HG2 H 0.85 0.02 2 33 5 4 VAL N N 120.9 0.2 1 34 6 5 ASP H H 8.25 0.02 1 35 6 5 ASP HA H 4.52 0.02 1 36 6 5 ASP HB2 H 2.53 0.02 2 37 6 5 ASP HB3 H 2.78 0.02 2 38 6 5 ASP N N 119.9 0.2 1 39 7 6 DLE N N 121.0 0.2 1 40 7 6 DLE H H 7.54 0.02 1 41 7 6 DLE HA H 4.47 0.02 1 42 7 6 DLE HB2 H 1.48 0.02 2 43 7 6 DLE HB3 H 1.52 0.02 2 44 7 6 DLE HG H 1.63 0.02 1 45 7 6 DLE HD11 H 0.85 0.02 2 46 7 6 DLE HD12 H 0.85 0.02 2 47 7 6 DLE HD13 H 0.85 0.02 2 48 7 6 DLE HD21 H 0.88 0.02 2 49 7 6 DLE HD22 H 0.88 0.02 2 50 7 6 DLE HD23 H 0.88 0.02 2 51 8 7 LEU H H 8.14 0.02 1 52 8 7 LEU HA H 4.51 0.02 1 53 8 7 LEU HB2 H 1.59 0.02 2 54 8 7 LEU HB3 H 1.61 0.02 2 55 8 7 LEU HG H 1.69 0.02 1 56 8 7 LEU HD1 H 0.85 0.02 2 57 8 7 LEU HD2 H 0.90 0.02 2 58 8 7 LEU N N 118.9 0.2 1 stop_ save_