data_11072 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; The solution structure of the N-terminal fragment of big defensin ; _BMRB_accession_number 11072 _BMRB_flat_file_name bmr11072.str _Entry_type new _Submission_date 2009-04-13 _Accession_date 2009-04-14 _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 Kouno Takahide . . 2 Mizuguchi Mineyuki . . 3 Aizawa Tomoyasu . . 4 Shinoda Hiroyuki . . 5 Demura Makoto . . 6 Kawabata Shun-ichiro . . 7 Kawano Keiichi . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 141 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2009-08-28 update BMRB 'complete entry citation' 2009-07-14 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_1 _Saveframe_category entry_citation _Citation_full . _Citation_title 'A novel beta-defensin structure: big defensin changes its N-terminal structure to associate with the target membrane.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19588912 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Kouno Takahide . . 2 Mizuguchi Mineyuki . . 3 Aizawa Tomoyasu . . 4 Shinoda Hiroyuki . . 5 Demura Makoto . . 6 Kawabata Shun-ichiro . . 7 Kawano Keiichi . . stop_ _Journal_abbreviation Biochemistry _Journal_volume 48 _Journal_issue 32 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 7629 _Page_last 7635 _Year 2009 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name big-N _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'A chain' $big-N 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_big-N _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'A chain' _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; PAIYIGATVGPSVWAYLVAL VGAAAVTAAN ; loop_ _Residue_seq_code _Residue_label 1 PRO 2 ALA 3 ILE 4 TYR 5 ILE 6 GLY 7 ALA 8 THR 9 VAL 10 GLY 11 PRO 12 SER 13 VAL 14 TRP 15 ALA 16 TYR 17 LEU 18 VAL 19 ALA 20 LEU 21 VAL 22 GLY 23 ALA 24 ALA 25 ALA 26 VAL 27 THR 28 ALA 29 ALA 30 ASN stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2014-11-10 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 BMRB 11022 "antimicrobial protein" 100.00 79 100.00 100.00 1.90e-09 PDB 2RNG "Solution Structure Of Big Defensin" 100.00 79 100.00 100.00 1.90e-09 PDB 2RQ2 "The Solution Structure Of The N-Terminal Fragment Of Big Defensin" 100.00 30 100.00 100.00 5.82e-09 GB AAB36095 "defensin, tachyplesin=anti-LPS factor [Tachypleus tridentatus, hemolymph plasma, hemocytes, Peptide, 79 aa]" 100.00 79 100.00 100.00 1.90e-09 PRF 2108380A "big defensin" 100.00 79 100.00 100.00 1.90e-09 PRF 2112271A "big defensin" 100.00 79 100.00 100.00 1.90e-09 SP P80957 "RecName: Full=Big defensin; Flags: Precursor [Tachypleus tridentatus]" 100.00 117 100.00 100.00 1.50e-09 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $big-N 'Japanese horseshoe crab' 6853 Eukaryota Metazoa Tachypleus tridentatus 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 $big-N '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 _Concentration_min_value _Concentration_max_value _Isotopic_labeling $big-N . mM 0.30 0.35 'natural abundance' SDS 100 mM . . '[U-99% 2H]' 'acetic acid' 50 mM . . '[U-99% 2H]' 'sodium chloride' 20 mM . . 'natural abundance' H2O 95 % . . . D2O 5 % . . . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Concentration_min_value _Concentration_max_value _Isotopic_labeling $big-N . mM 0.30 0.35 'natural abundance' SDS 100 mM . . '[U-99% 2H]' 'acetic acid' 50 mM . . '[U-99% 2H]' 'sodium chloride' 20 mM . . 'natural abundance' D2O 100 % . . . stop_ save_ ############################ # Computer software used # ############################ save_xwinnmr _Saveframe_category software _Name xwinnmr _Version . loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection stop_ _Details . save_ 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_SPARKY _Saveframe_category software _Name SPARKY _Version . loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' 'peak picking' 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 Avance _Field_strength 800 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_COSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H COSY' _Sample_label $sample_2 save_ save_2D_1H-1H_TOCSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_2 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 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 . K pH 3.5 . 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' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name 'A chain' _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 PRO HA H 4.48 0.02 1 2 1 1 PRO HB2 H 2.06 0.02 1 3 1 1 PRO HB3 H 2.51 0.02 1 4 1 1 PRO HD2 H 3.45 0.02 1 5 1 1 PRO HD3 H 3.45 0.02 1 6 1 1 PRO HG2 H 1.97 0.02 1 7 1 1 PRO HG3 H 2.06 0.02 1 8 2 2 ALA H H 8.53 0.02 1 9 2 2 ALA HA H 4.40 0.02 1 10 2 2 ALA HB H 1.36 0.02 1 11 3 3 ILE H H 7.66 0.02 1 12 3 3 ILE HA H 4.16 0.02 1 13 3 3 ILE HB H 1.82 0.02 1 14 3 3 ILE HD1 H 0.86 0.02 1 15 3 3 ILE HG12 H 1.12 0.02 1 16 3 3 ILE HG13 H 1.43 0.02 1 17 3 3 ILE HG2 H 0.86 0.02 1 18 4 4 TYR H H 7.95 0.02 1 19 4 4 TYR HA H 4.65 0.02 1 20 4 4 TYR HB2 H 2.97 0.02 1 21 4 4 TYR HB3 H 3.04 0.02 1 22 4 4 TYR HD1 H 7.13 0.02 1 23 4 4 TYR HD2 H 7.13 0.02 1 24 4 4 TYR HE1 H 6.81 0.02 1 25 4 4 TYR HE2 H 6.81 0.02 1 26 5 5 ILE H H 7.86 0.02 1 27 5 5 ILE HA H 4.10 0.02 1 28 5 5 ILE HB H 1.92 0.02 1 29 5 5 ILE HD1 H 0.90 0.02 1 30 5 5 ILE HG12 H 1.18 0.02 1 31 5 5 ILE HG13 H 1.48 0.02 1 32 5 5 ILE HG2 H 0.91 0.02 1 33 6 6 GLY H H 7.94 0.02 1 34 6 6 GLY HA2 H 3.82 0.02 1 35 6 6 GLY HA3 H 3.91 0.02 1 36 7 7 ALA H H 7.81 0.02 1 37 7 7 ALA HA H 4.35 0.02 1 38 7 7 ALA HB H 1.43 0.02 1 39 8 8 THR H H 8.03 0.02 1 40 8 8 THR HA H 4.40 0.02 1 41 8 8 THR HB H 4.30 0.02 1 42 8 8 THR HG2 H 1.24 0.02 1 43 9 9 VAL H H 7.99 0.02 1 44 9 9 VAL HA H 4.14 0.02 1 45 9 9 VAL HB H 2.21 0.02 1 46 9 9 VAL HG1 H 0.97 0.02 1 47 9 9 VAL HG2 H 0.99 0.02 1 48 10 10 GLY H H 8.34 0.02 1 49 10 10 GLY HA2 H 3.90 0.02 1 50 10 10 GLY HA3 H 4.15 0.02 1 51 11 11 PRO HA H 4.43 0.02 1 52 11 11 PRO HB2 H 2.50 0.02 1 53 11 11 PRO HB3 H 2.01 0.02 1 54 11 11 PRO HD2 H 3.68 0.02 1 55 11 11 PRO HD3 H 3.68 0.02 1 56 11 11 PRO HG2 H 2.16 0.02 1 57 11 11 PRO HG3 H 2.16 0.02 1 58 12 12 SER H H 7.93 0.02 1 59 12 12 SER HA H 4.44 0.02 1 60 12 12 SER HB2 H 4.11 0.02 1 61 12 12 SER HB3 H 3.97 0.02 1 62 13 13 VAL H H 8.18 0.02 1 63 13 13 VAL HA H 3.77 0.02 1 64 13 13 VAL HB H 2.28 0.02 1 65 13 13 VAL HG1 H 1.01 0.02 1 66 13 13 VAL HG2 H 1.06 0.02 1 67 14 14 TRP H H 8.37 0.02 1 68 14 14 TRP HA H 4.53 0.02 1 69 14 14 TRP HB2 H 3.34 0.02 1 70 14 14 TRP HB3 H 3.34 0.02 1 71 14 14 TRP HD1 H 7.20 0.02 1 72 14 14 TRP HE3 H 7.42 0.02 1 73 14 14 TRP HH2 H 7.03 0.02 1 74 14 14 TRP HZ2 H 7.38 0.02 1 75 14 14 TRP HZ3 H 6.90 0.02 1 76 15 15 ALA H H 7.96 0.02 1 77 15 15 ALA HA H 3.95 0.02 1 78 15 15 ALA HB H 1.52 0.02 1 79 16 16 TYR H H 7.78 0.02 1 80 16 16 TYR HA H 4.18 0.02 1 81 16 16 TYR HB2 H 3.23 0.02 1 82 16 16 TYR HB3 H 3.20 0.02 1 83 16 16 TYR HD1 H 7.05 0.02 1 84 16 16 TYR HD2 H 7.05 0.02 1 85 16 16 TYR HE1 H 6.77 0.02 1 86 16 16 TYR HE2 H 6.77 0.02 1 87 17 17 LEU H H 8.24 0.02 1 88 17 17 LEU HA H 3.96 0.02 1 89 17 17 LEU HB2 H 1.93 0.02 1 90 17 17 LEU HB3 H 1.87 0.02 1 91 17 17 LEU HG H 1.41 0.02 1 92 18 18 VAL H H 8.37 0.02 1 93 18 18 VAL HA H 3.29 0.02 1 94 18 18 VAL HB H 1.77 0.02 1 95 18 18 VAL HG1 H 0.73 0.02 1 96 18 18 VAL HG2 H 0.42 0.02 1 97 19 19 ALA H H 7.48 0.02 1 98 19 19 ALA HA H 4.09 0.02 1 99 19 19 ALA HB H 1.42 0.02 1 100 20 20 LEU H H 7.97 0.02 1 101 20 20 LEU HA H 4.03 0.02 1 102 20 20 LEU HB2 H 1.68 0.02 1 103 20 20 LEU HB3 H 1.68 0.02 1 104 20 20 LEU HD1 H 0.88 0.02 1 105 20 20 LEU HD2 H 0.86 0.02 1 106 20 20 LEU HG H 1.60 0.02 1 107 21 21 VAL H H 8.21 0.02 1 108 21 21 VAL HA H 3.68 0.02 1 109 21 21 VAL HB H 2.12 0.02 1 110 21 21 VAL HG1 H 0.96 0.02 1 111 21 21 VAL HG2 H 1.00 0.02 1 112 22 22 GLY H H 8.11 0.02 1 113 22 22 GLY HA2 H 3.87 0.02 1 114 22 22 GLY HA3 H 3.85 0.02 1 115 23 23 ALA H H 7.76 0.02 1 116 23 23 ALA HA H 4.26 0.02 1 117 23 23 ALA HB H 1.48 0.02 1 118 24 24 ALA H H 7.96 0.02 1 119 24 24 ALA HA H 4.20 0.02 1 120 24 24 ALA HB H 1.49 0.02 1 121 25 25 ALA H H 8.19 0.02 1 122 25 25 ALA HA H 4.20 0.02 1 123 25 25 ALA HB H 1.47 0.02 1 124 26 26 VAL H H 7.70 0.02 1 125 26 26 VAL HA H 4.02 0.02 1 126 26 26 VAL HB H 2.21 0.02 1 127 26 26 VAL HG1 H 0.99 0.02 1 128 26 26 VAL HG2 H 1.03 0.02 1 129 27 27 THR H H 7.87 0.02 1 130 27 27 THR HA H 4.23 0.02 1 131 27 27 THR HB H 4.28 0.02 1 132 27 27 THR HG2 H 1.24 0.02 1 133 28 28 ALA H H 8.06 0.02 1 134 28 28 ALA HA H 4.28 0.02 1 135 28 28 ALA HB H 1.43 0.02 1 136 29 29 ALA H H 7.91 0.02 1 137 29 29 ALA HA H 4.31 0.02 1 138 29 29 ALA HB H 1.42 0.02 1 139 30 30 ASN H H 7.96 0.02 1 140 30 30 ASN HB2 H 2.78 0.02 1 141 30 30 ASN HB3 H 2.86 0.02 1 stop_ save_