data_18879 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SP-B C-terminal (residues 59-80) peptide in DPC micelles ; _BMRB_accession_number 18879 _BMRB_flat_file_name bmr18879.str _Entry_type original _Submission_date 2012-12-06 _Accession_date 2012-12-06 _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 Kuznetsova Anna . . 2 Vanni Julieann . . 3 Long Joanna . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 131 "15N chemical shifts" 24 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2013-12-16 original author . stop_ _Original_release_date 2013-12-16 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Solution NMR structures of the C-terminal segment of surfactant protein B (residues 59-80) in DPC detergent micelles and methanol.' _Citation_status submitted _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kuznetsova Anna . . 2 Vanni Julieann . . 3 Long Joanna R. . stop_ _Journal_abbreviation Biochemistry _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'SP-B C-terminal (residues 59-80) peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label SP-B $entity 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_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common entity _Molecular_mass 2500.072 _Mol_thiol_state . _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 22 _Mol_residue_sequence ; DTLLGRILPQLVCRLVLRCS ID ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 59 ASP 2 60 THR 3 61 LEU 4 62 LEU 5 63 GLY 6 64 ARG 7 65 ILE 8 66 LEU 9 67 PRO 10 68 GLN 11 69 LEU 12 70 VAL 13 71 CYS 14 72 ARG 15 73 LEU 16 74 VAL 17 75 LEU 18 76 ARG 19 77 CYS 20 78 SER 21 79 ILE 22 80 ASP stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-02-23 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2M1T "Sp-b C-terminal (residues 59-80) Peptide In Dpc Micelles" 100.00 22 100.00 100.00 3.56e-05 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $entity 'E. coli' 562 Bacteria . Escherichia coli BL21(DE3)pLysS 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 $entity 'recombinant technology' . Escherichia coli BL21(DE3)pLysS pET31b stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_SP-B_residues_59-80_in_DPC_micelles _Saveframe_category sample _Sample_type solution _Details '1.2mM SP-B residues 59-80 in 80mM DPC-d38, pH 4.5, 50mM phosphate buffer, 5% D2O, reduced with 20mM TCEP, final sample volume 110uL' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 1.2 mM '[U-100% 15N]' D2O 5 % '[U-100% 2H]' DPC 80 mM '[U-100% 2H]' TSP 1 mM 'natural abundance' 'sodium phosphate' 50 mM 'natural abundance' H2O 95 % 'natural abundance' 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 'data analysis' processing stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.32 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement 'structure solution' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection 'data analysis' stop_ _Details . save_ save_MOLPROBITY _Saveframe_category software _Name MolProbity _Version . loop_ _Vendor _Address _Electronic_address 'Ian W. Davis, Vincent B. Chen, Robert M. Immormino et. al' . http://molprobity.biochem.duke.edu/ stop_ loop_ _Task 'evaluation of structure refinement' 'structure evaluation' 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-15N_HSQC_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-15N HSQC' _Sample_label $SP-B_residues_59-80_in_DPC_micelles save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $SP-B_residues_59-80_in_DPC_micelles save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $SP-B_residues_59-80_in_DPC_micelles save_ save_3D_1H-15N_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N TOCSY' _Sample_label $SP-B_residues_59-80_in_DPC_micelles save_ save_3D_1H-15N_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 1H-15N NOESY' _Sample_label $SP-B_residues_59-80_in_DPC_micelles save_ save_NMR_spectrometer_expt _Saveframe_category NMR_applied_experiment _Experiment_name . _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_315K _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 130 30 mM pH 4.5 0.5 pH pressure 1 . atm temperature 315 . 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 TSP H 1 'methyl protons' ppm 0 internal direct . . . 1.000000000 TSP N 15 'methyl protons' ppm 0 internal 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 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-15N HSQC' '2D 1H-1H TOCSY' '2D 1H-1H NOESY' '3D 1H-15N TOCSY' '3D 1H-15N NOESY' stop_ loop_ _Sample_label $SP-B_residues_59-80_in_DPC_micelles stop_ _Sample_conditions_label $315K _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name SP-B _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 59 1 ASP HA H 4.650 0.010 1 2 59 1 ASP HB2 H 3.045 0.005 2 3 59 1 ASP HB3 H 3.045 0.005 2 4 60 2 THR H H 8.767 0.002 1 5 60 2 THR HA H 4.510 0.010 1 6 60 2 THR HB H 4.480 0.010 1 7 60 2 THR HG2 H 1.275 0.010 1 8 60 2 THR N N 115.1 0.1 1 9 61 3 LEU H H 8.908 0.002 1 10 61 3 LEU HA H 4.156 0.005 1 11 61 3 LEU HB2 H 1.875 0.010 2 12 61 3 LEU HB3 H 1.800 0.005 2 13 61 3 LEU HG H 1.666 0.010 1 14 61 3 LEU HD1 H 0.918 0.003 2 15 61 3 LEU HD2 H 0.965 0.003 2 16 61 3 LEU N N 124.1 0.1 1 17 62 4 LEU H H 8.505 0.002 1 18 62 4 LEU HA H 4.020 0.005 1 19 62 4 LEU HB2 H 1.770 0.010 2 20 62 4 LEU HB3 H 1.740 0.005 2 21 62 4 LEU HG H 1.527 0.005 1 22 62 4 LEU HD1 H 0.865 0.003 2 23 62 4 LEU HD2 H 0.943 0.003 2 24 62 4 LEU N N 117.9 0.1 1 25 63 5 GLY H H 8.060 0.003 1 26 63 5 GLY HA2 H 3.935 0.010 2 27 63 5 GLY HA3 H 3.775 0.010 2 28 63 5 GLY N N 104.7 0.1 1 29 64 6 ARG H H 7.670 0.002 1 30 64 6 ARG HA H 4.400 0.005 1 31 64 6 ARG HB2 H 1.952 0.004 2 32 64 6 ARG HB3 H 1.760 0.004 2 33 64 6 ARG HG2 H 1.650 0.004 2 34 64 6 ARG HG3 H 1.650 0.004 2 35 64 6 ARG HD2 H 3.204 0.002 2 36 64 6 ARG HD3 H 3.204 0.002 2 37 64 6 ARG HE H 7.363 0.001 1 38 64 6 ARG N N 117.2 0.1 1 39 64 6 ARG NE N 84.3 0.1 1 40 65 7 ILE H H 8.005 0.003 1 41 65 7 ILE HA H 4.092 0.004 1 42 65 7 ILE HB H 1.940 0.005 1 43 65 7 ILE HG12 H 1.300 0.003 2 44 65 7 ILE HG13 H 1.255 0.003 2 45 65 7 ILE HG2 H 0.910 0.003 1 46 65 7 ILE HD1 H 0.840 0.003 1 47 65 7 ILE N N 116.5 0.1 1 48 66 8 LEU H H 8.367 0.002 1 49 66 8 LEU HA H 4.245 0.004 1 50 66 8 LEU HB2 H 1.910 0.005 2 51 66 8 LEU HB3 H 1.800 0.003 2 52 66 8 LEU HG H 1.615 0.003 1 53 66 8 LEU HD1 H 0.873 0.002 2 54 66 8 LEU HD2 H 0.920 0.002 2 55 66 8 LEU N N 119.7 0.1 1 56 67 9 PRO HB2 H 1.930 0.020 2 57 67 9 PRO HB3 H 1.930 0.020 2 58 67 9 PRO HD2 H 3.655 0.020 2 59 67 9 PRO HD3 H 3.600 0.020 2 60 68 10 GLN H H 7.245 0.003 1 61 68 10 GLN HA H 4.055 0.004 1 62 68 10 GLN HB2 H 2.220 0.002 2 63 68 10 GLN HB3 H 2.130 0.002 2 64 68 10 GLN HG2 H 2.477 0.002 2 65 68 10 GLN HG3 H 2.445 0.002 2 66 68 10 GLN HE21 H 6.840 0.003 2 67 68 10 GLN HE22 H 7.460 0.003 2 68 68 10 GLN N N 114.4 0.05 1 69 68 10 GLN NE2 N 110.9 0.1 1 70 69 11 LEU H H 8.060 0.002 1 71 69 11 LEU HA H 4.070 0.004 1 72 69 11 LEU HB2 H 1.860 0.004 2 73 69 11 LEU HB3 H 1.770 0.003 2 74 69 11 LEU HG H 1.650 0.004 1 75 69 11 LEU HD1 H 0.830 0.003 2 76 69 11 LEU HD2 H 0.870 0.003 2 77 69 11 LEU N N 119.1 0.1 1 78 70 12 VAL H H 8.328 0.002 1 79 70 12 VAL HA H 3.535 0.005 1 80 70 12 VAL HB H 2.140 0.004 1 81 70 12 VAL HG1 H 1.020 0.003 2 82 70 12 VAL HG2 H 0.930 0.003 2 83 70 12 VAL N N 117.2 0.1 1 84 71 13 CYS H H 8.058 0.003 1 85 71 13 CYS HA H 4.660 0.020 1 86 71 13 CYS HB2 H 3.140 0.020 2 87 71 13 CYS HB3 H 3.465 0.020 2 88 71 13 CYS N N 116.8 0.1 1 89 72 14 ARG H H 7.771 0.002 1 90 72 14 ARG HA H 4.370 0.005 1 91 72 14 ARG HB2 H 1.940 0.005 2 92 72 14 ARG HB3 H 1.940 0.005 2 93 72 14 ARG HG2 H 1.760 0.005 2 94 72 14 ARG HG3 H 1.760 0.005 2 95 72 14 ARG HD2 H 3.193 0.002 2 96 72 14 ARG HD3 H 3.193 0.002 2 97 72 14 ARG HE H 7.582 0.002 1 98 72 14 ARG N N 117.2 0.1 1 99 72 14 ARG NE N 84.3 0.1 1 100 73 15 LEU H H 7.853 0.002 5 101 73 15 LEU HA H 4.445 0.004 5 102 73 15 LEU HB2 H 1.760 0.004 5 103 73 15 LEU HB3 H 1.870 0.004 5 104 73 15 LEU HG H 1.566 0.004 5 105 73 15 LEU HD1 H 0.877 0.003 5 106 73 15 LEU HD2 H 0.877 0.003 5 107 73 15 LEU N N 115.3 0.1 5 108 74 16 VAL H H 7.706 0.002 1 109 74 16 VAL HA H 4.350 0.004 1 110 74 16 VAL HB H 2.335 0.004 1 111 74 16 VAL HG1 H 1.055 0.002 2 112 74 16 VAL HG2 H 0.936 0.003 2 113 74 16 VAL N N 112.2 0.1 1 114 75 17 LEU H H 7.853 0.002 5 115 75 17 LEU HA H 4.445 0.004 5 116 75 17 LEU HB2 H 1.760 0.004 5 117 75 17 LEU HB3 H 1.870 0.004 5 118 75 17 LEU HG H 1.566 0.004 5 119 75 17 LEU HD1 H 0.877 0.003 5 120 75 17 LEU HD2 H 0.877 0.003 5 121 75 17 LEU N N 115.3 0.1 5 122 76 18 ARG H H 7.913 0.002 1 123 76 18 ARG HA H 4.475 0.004 1 124 76 18 ARG HB2 H 1.710 0.005 2 125 76 18 ARG HB3 H 1.850 0.002 2 126 76 18 ARG HG2 H 1.560 0.005 2 127 76 18 ARG HG3 H 1.630 0.004 2 128 76 18 ARG HD2 H 3.178 0.002 2 129 76 18 ARG HD3 H 3.178 0.002 2 130 76 18 ARG HE H 7.313 0.002 1 131 76 18 ARG N N 118.2 0.1 1 132 76 18 ARG NE N 85.0 0.1 1 133 77 19 CYS H H 8.440 0.002 1 134 77 19 CYS HA H 4.560 0.004 1 135 77 19 CYS HB2 H 3.170 0.010 2 136 77 19 CYS HB3 H 3.415 0.010 2 137 77 19 CYS N N 120.6 0.1 1 138 78 20 SER H H 8.460 0.003 1 139 78 20 SER HA H 4.455 0.005 1 140 78 20 SER HB2 H 3.840 0.005 2 141 78 20 SER HB3 H 3.840 0.005 2 142 78 20 SER N N 116.3 0.1 1 143 79 21 ILE H H 8.056 0.003 1 144 79 21 ILE HA H 4.170 0.005 1 145 79 21 ILE HB H 1.884 0.005 1 146 79 21 ILE HG12 H 1.165 0.005 2 147 79 21 ILE HG13 H 1.435 0.005 2 148 79 21 ILE HG2 H 0.893 0.003 1 149 79 21 ILE HD1 H 0.845 0.003 1 150 79 21 ILE N N 121.0 0.1 1 151 80 22 ASP H H 8.353 0.002 1 152 80 22 ASP HA H 4.720 0.005 1 153 80 22 ASP HB2 H 2.780 0.006 2 154 80 22 ASP HB3 H 2.930 0.006 2 155 80 22 ASP N N 121.0 0.1 1 stop_ loop_ _Atom_shift_assign_ID_ambiguity 100,114 101,115 102,103,116,117 104,118 105,106,119,120 107,121 stop_ save_