data_6420 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Daptomycin NMR Structure ; _BMRB_accession_number 6420 _BMRB_flat_file_name bmr6420.str _Entry_type original _Submission_date 2004-12-10 _Accession_date 2004-12-10 _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 Ball L.-J. . . 2 Goult C. M. . 3 Donarski J. A. . 4 Micklefield J. . . 5 Ramesh V. . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 60 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2008-07-17 update BMRB 'Updating non-standard residue' stop_ _Original_release_date 2004-12-10 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; NMR structure determination and calcium binding effects of lipopeptide antibiotic daptomycin. ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 15227539 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Ball L.-J. . . 2 Goult C. M. . 3 Donarski J. A. . 4 Micklefield J. . . 5 Ramesh V. . . stop_ _Journal_abbreviation 'Org. Biomol. Chem.' _Journal_volume 2 _Journal_issue 13 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 1872 _Page_last 1878 _Year 2004 _Details . loop_ _Keyword ANTIBIOTIC LIPOPEPTIDE stop_ save_ ################################## # Molecular system description # ################################## save_system_Daptomycin _Saveframe_category molecular_system _Mol_system_name Daptomycin _Abbreviation_common Daptomycin _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label Daptomycin $Daptomycin stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_Daptomycin _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common Daptomycin _Abbreviation_common Daptomycin _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 14 _Mol_residue_sequence ; XWNDTGXDXDGXXX ; loop_ _Residue_seq_code _Residue_label 1 DKA 2 TRP 3 ASN 4 ASP 5 THR 6 GLY 7 ORN 8 ASP 9 DAL 10 ASP 11 GLY 12 DSN 13 LME 14 KYN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ ###################### # Polymer residues # ###################### save_chem_comp_DKA _Saveframe_category polymer_residue _Mol_type non-polymer _Name_common 'DECANOIC ACID' _BMRB_code . _PDB_code DKA _Standard_residue_derivative . _Molecular_mass 172.265 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 1 10:39:31 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C1 C1 C . 0 . ? O1 O1 O . 0 . ? C2 C2 C . 0 . ? C3 C3 C . 0 . ? C4 C4 C . 0 . ? C5 C5 C . 0 . ? C6 C6 C . 0 . ? C7 C7 C . 0 . ? C8 C8 C . 0 . ? C9 C9 C . 0 . ? C10 C10 C . 0 . ? O2 O2 O . 0 . ? H21 H21 H . 0 . ? H22 H22 H . 0 . ? H31 H31 H . 0 . ? H32 H32 H . 0 . ? H41 H41 H . 0 . ? H42 H42 H . 0 . ? H51 H51 H . 0 . ? H52 H52 H . 0 . ? H61 H61 H . 0 . ? H62 H62 H . 0 . ? H71 H71 H . 0 . ? H72 H72 H . 0 . ? H81 H81 H . 0 . ? H82 H82 H . 0 . ? H91 H91 H . 0 . ? H92 H92 H . 0 . ? H101 H101 H . 0 . ? H102 H102 H . 0 . ? H103 H103 H . 0 . ? HO2 HO2 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 DOUB C1 O1 ? ? SING C1 C2 ? ? SING C1 O2 ? ? SING C2 C3 ? ? SING C2 H21 ? ? SING C2 H22 ? ? SING C3 C4 ? ? SING C3 H31 ? ? SING C3 H32 ? ? SING C4 C5 ? ? SING C4 H41 ? ? SING C4 H42 ? ? SING C5 C6 ? ? SING C5 H51 ? ? SING C5 H52 ? ? SING C6 C7 ? ? SING C6 H61 ? ? SING C6 H62 ? ? SING C7 C8 ? ? SING C7 H71 ? ? SING C7 H72 ? ? SING C8 C9 ? ? SING C8 H81 ? ? SING C8 H82 ? ? SING C9 C10 ? ? SING C9 H91 ? ? SING C9 H92 ? ? SING C10 H101 ? ? SING C10 H102 ? ? SING C10 H103 ? ? SING O2 HO2 ? ? stop_ save_ save_chem_comp_ORN _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common L-ornithine _BMRB_code . _PDB_code ORN _Standard_residue_derivative . _Molecular_mass 132.161 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 1 15:05:30 2011 ; 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 . ? CD CD C . 0 . ? NE NE N . 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 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HD2 HD2 H . 0 . ? HD3 HD3 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 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 CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? SING CD NE ? ? SING CD HD2 ? ? SING CD HD3 ? ? SING NE HE1 ? ? SING NE HE2 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DAL _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-ALANINE _BMRB_code . _PDB_code DAL _Standard_residue_derivative . _Molecular_mass 89.093 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 1 10:26:43 2011 ; 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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HB1 HB1 H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 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 HB1 ? ? SING CB HB2 ? ? SING CB HB3 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_DSN _Saveframe_category polymer_residue _Mol_type 'D-peptide linking' _Name_common D-SERINE _BMRB_code . _PDB_code DSN _Standard_residue_derivative . _Molecular_mass 105.093 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 1 10:28:19 2011 ; 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 . ? C C C . 0 . ? O O O . 0 . ? OXT OXT O . 0 . ? CB CB C . 0 . ? OG OG O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HA HA H . 0 . ? HXT HXT H . 0 . ? HB2 HB2 H . 0 . ? HB3 HB3 H . 0 . ? HG HG 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 C ? ? SING CA CB ? ? SING CA HA ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? SING CB OG ? ? SING CB HB2 ? ? SING CB HB3 ? ? SING OG HG ? ? stop_ save_ save_chem_comp_LME _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common '(2S,3R)-2-azanyl-3-methyl-pentanedioic acid' _BMRB_code . _PDB_code LME _Standard_residue_derivative . _Molecular_mass 161.156 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 1 15:08:33 2011 ; 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 . ? C1 C1 C . 0 . ? CG CG C . 0 . ? CD CD C . 0 . ? OE1 OE1 O . 0 . ? OE2 OE2 O . 0 . ? C C C . 0 . ? O O O . 0 . ? H2 H2 H . 0 . ? H H H . 0 . ? HA HA H . 0 . ? HB HB H . 0 . ? H11 H11 H . 0 . ? H12 H12 H . 0 . ? H13 H13 H . 0 . ? HG2 HG2 H . 0 . ? HG3 HG3 H . 0 . ? HE2 HE2 H . 0 . ? OXT OXT O . 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 H2 ? ? SING N H ? ? SING CA CB ? ? SING CA C ? ? SING CA HA ? ? SING CB C1 ? ? SING CB CG ? ? SING CB HB ? ? SING C1 H11 ? ? SING C1 H12 ? ? SING C1 H13 ? ? SING CG CD ? ? SING CG HG2 ? ? SING CG HG3 ? ? DOUB CD OE1 ? ? SING CD OE2 ? ? SING OE2 HE2 ? ? DOUB C O ? ? SING C OXT ? ? SING OXT HXT ? ? stop_ save_ save_chem_comp_KYN _Saveframe_category polymer_residue _Mol_type 'L-peptide linking' _Name_common '(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid' _BMRB_code . _PDB_code KYN _Standard_residue_derivative . _Molecular_mass 208.214 _Mol_paramagnetic . _Details ; Information obtained from PDB's Chemical Component Dictionary at http://wwpdb-remediation.rutgers.edu/downloads.html Downloaded on Mon Aug 1 10:37:42 2011 ; loop_ _Atom_name _PDB_atom_name _Atom_type _Atom_chirality _Atom_charge _Atom_oxidation_number _Atom_unpaired_electrons C C C . 0 . ? N N N . 0 . ? OXT OXT O . 0 . ? C1 C1 C . 0 . ? N1 N1 N . 0 . ? O2 O2 O . 0 . ? CA CA C . 0 . ? CB CB C . 0 . ? CG CG C . 0 . ? CZ CZ C . 0 . ? CD1 CD1 C . 0 . ? CD2 CD2 C . 0 . ? CE1 CE1 C . 0 . ? CE2 CE2 C . 0 . ? O O O . 0 . ? H H H . 0 . ? H2 H2 H . 0 . ? HXT HXT H . 0 . ? HN1 HN1 H . 0 . ? HN1A HN1A H . 0 . ? HA HA H . 0 . ? HB HB H . 0 . ? HBA HBA H . 0 . ? HZ HZ H . 0 . ? HD1 HD1 H . 0 . ? HE1 HE1 H . 0 . ? HE2 HE2 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 CA C ? ? DOUB O C ? ? SING C OXT ? ? SING N CA ? ? SING N H ? ? SING N H2 ? ? SING OXT HXT ? ? SING CD2 C1 ? ? DOUB O2 C1 ? ? SING C1 CB ? ? SING CG N1 ? ? SING N1 HN1 ? ? SING N1 HN1A ? ? SING CB CA ? ? SING CA HA ? ? SING CB HB ? ? SING CB HBA ? ? DOUB CD1 CG ? ? SING CD2 CG ? ? DOUB CZ CE1 ? ? SING CZ CE2 ? ? SING CZ HZ ? ? SING CE1 CD1 ? ? SING CD1 HD1 ? ? DOUB CE2 CD2 ? ? SING CE1 HE1 ? ? SING CE2 HE2 ? ? stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $Daptomycin . . . . . . 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 $Daptomycin 'chemical synthesis' . . . . . 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 $Daptomycin 0.8 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name xwinnmr _Version 3.5 loop_ _Task collection stop_ _Details Bruker save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 1.0 loop_ _Task processing stop_ _Details 'Delagio, F.' save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.0 loop_ _Task 'data analysis' stop_ _Details 'Goddard, T.D.' save_ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task refinement 'structure solution' stop_ _Details 'Guntert, P.' save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.05 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 . H 1 . ppm . . . . . . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name Daptomycin _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 TRP HA H 4.609 0.000 . 2 . 2 TRP HB2 H 3.166 0.000 . 3 . 2 TRP HB3 H 3.255 0.000 . 4 . 2 TRP HD1 H 7.258 0.000 . 5 . 2 TRP HE3 H 7.620 0.000 . 6 . 2 TRP HH2 H 7.163 0.000 . 7 . 2 TRP HZ2 H 7.438 0.000 . 8 . 2 TRP HZ3 H 7.067 0.000 . 9 . 2 TRP H H 8.012 0.000 . 10 . 3 ASN HA H 4.513 0.000 . 11 . 3 ASN HB2 H 2.519 0.000 . 12 . 3 ASN HB3 H 2.432 0.000 . 13 . 3 ASN H H 8.257 0.000 . 14 . 4 ASP HA H 4.686 0.000 . 15 . 4 ASP HB2 H 2.665 0.000 . 16 . 4 ASP HB3 H 2.801 0.000 . 17 . 4 ASP H H 8.291 0.000 . 18 . 5 THR HA H 4.672 0.000 . 19 . 5 THR HB H 5.475 0.000 . 20 . 5 THR H H 8.122 0.000 . 21 . 5 THR HG2 H 1.166 0.000 . 22 . 6 GLY HA2 H 4.070 0.000 . 23 . 6 GLY HA3 H 4.018 0.000 . 24 . 6 GLY H H 8.313 0.000 . 25 . 7 ORN HA H 4.362 0.000 . 26 . 7 ORN HB2 H 1.891 0.000 . 27 . 7 ORN HB3 H 1.793 0.000 . 28 . 7 ORN HG2 H 1.713 0.000 . 29 . 7 ORN HD2 H 2.997 0.000 . 30 . 7 ORN H H 8.297 0.000 . 31 . 8 ASP HA H 4.537 0.000 . 32 . 8 ASP HB2 H 2.404 0.000 . 33 . 8 ASP HB3 H 2.581 0.000 . 34 . 8 ASP H H 8.341 0.000 . 35 . 9 DAL HA H 4.318 0.000 . 36 . 9 DAL HB H 1.363 0.000 . 37 . 9 DAL H H 8.187 0.000 . 38 . 10 ASP HA H 4.654 0.000 . 39 . 10 ASP HB2 H 2.708 0.000 . 40 . 10 ASP HB3 H 2.774 0.000 . 41 . 10 ASP H H 8.459 0.000 . 42 . 11 GLY HA2 H 3.992 0.000 . 43 . 11 GLY H H 8.338 0.000 . 44 . 12 DSN HA H 4.584 0.000 . 45 . 12 DSN HB2 H 3.878 0.000 . 46 . 12 DSN H H 8.046 0.000 . 47 . 13 LME HA H 4.575 0.000 . 48 . 13 LME HB H 2.425 0.000 . 49 . 13 LME HG1 H 0.931 0.000 . 50 . 13 LME HG22 H 2.114 0.000 . 51 . 13 LME HG23 H 2.369 0.000 . 52 . 13 LME H H 8.275 0.000 . 53 . 14 KYN HA H 4.848 0.000 . 54 . 14 KYN HB2 H 3.258 0.000 . 55 . 14 KYN HB3 H 3.535 0.000 . 56 . 14 KYN HH H 7.357 0.000 . 57 . 14 KYN HI H 7.412 0.000 . 58 . 14 KYN HT H 6.683 0.000 . 59 . 14 KYN HZ H 6.793 0.000 . 60 . 14 KYN H H 8.520 0.000 . stop_ save_