data_16254 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; NMR Structure of human alpha defensin HNP-1 ; _BMRB_accession_number 16254 _BMRB_flat_file_name bmr16254.str _Entry_type original _Submission_date 2009-04-11 _Accession_date 2009-04-11 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'HNP-1 structure determination through 2D & 3D CC and NC correlation experiments by solid state NMR.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Zhang Yuan . . 2 Li Shenhui . . 3 Doherty Timothy F. . 4 Lubkowski Jacek . . 5 Lu Wuyuan . . 6 Li Jing . . 7 Barinka Cyril . . 8 Hong Mei . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "13C chemical shifts" 115 "15N chemical shifts" 30 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2010-02-10 update BMRB 'completed entry citation' 2010-01-12 original author 'original release' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title '3D (13)C-(13)C-(13)C correlation NMR for de novo distance determination of solid proteins and application to a human alpha-defensin.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 19963419 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Li Shenhui . . 2 Zhang Yuan . . 3 Hong Mei . . stop_ _Journal_abbreviation 'J. Magn. Reson.' _Journal_name_full 'Journal of magnetic resonance (San Diego, Calif. : 1997)' _Journal_volume 202 _Journal_issue 2 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 203 _Page_last 210 _Year 2010 _Details . loop_ _Keyword 'human alpha defensin' 'microcrystalline protein' 'resonance assignment' 'solid state NMR' 'structure determination' stop_ save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'Microcrystalline HNP-1' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label HNP-1 $HNP-1 stop_ _System_molecular_weight 3452.115 _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_HNP-1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common HNP-1 _Molecular_mass 3452.115 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 30 _Mol_residue_sequence ; ACYCRIPACIAGERRYGTCI YQGRLWAFCC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 2 ALA 2 3 CYS 3 4 TYR 4 5 CYS 5 6 ARG 6 7 ILE 7 8 PRO 8 9 ALA 9 10 CYS 10 11 ILE 11 12 ALA 12 13 GLY 13 14 GLU 14 15 ARG 15 16 ARG 16 17 TYR 17 18 GLY 18 19 THR 19 20 CYS 20 21 ILE 21 22 TYR 22 23 GLN 23 24 GLY 24 25 ARG 25 26 LEU 26 27 TRP 27 28 ALA 28 29 PHE 29 30 CYS 30 31 CYS stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-30 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 1DFN "Crystal Structure Of Defensin Hnp-3, An Amphiphilic Dimer: Mechanisms Of Membrane Permeabilization" 96.67 30 100.00 100.00 4.86e-11 PDB 2KHT "Nmr Structure Of Human Alpha Defensin Hnp-1" 100.00 30 100.00 100.00 1.60e-11 PDB 3GNY "Crystal Structure Of Human Alpha-Defensin 1 (Hnp1)" 100.00 30 100.00 100.00 1.60e-11 PDB 3HJ2 "Crystal Structure Of Covalent Dimer Of Hnp1" 100.00 33 100.00 100.00 2.21e-11 DBJ BAJ20578 "defensin, alpha 3, neutrophil-specific [synthetic construct]" 96.67 94 100.00 100.00 2.27e-12 EMBL CAA31952 "unnamed protein product [Homo sapiens]" 96.67 94 100.00 100.00 2.27e-12 EMBL CAA36280 "unnamed protein product [Homo sapiens]" 100.00 94 100.00 100.00 7.14e-13 GB AAA35753 "neutrophil peptide 3 precursor [Homo sapiens]" 96.67 65 100.00 100.00 5.56e-12 GB AAA36382 "neutrophil peptide-1 [Homo sapiens]" 100.00 94 100.00 100.00 7.14e-13 GB AAA52302 "neutrophil peptide 1 precursor [Homo sapiens]" 100.00 94 100.00 100.00 7.14e-13 GB AAA52303 "defensin 1 [Homo sapiens]" 100.00 94 100.00 100.00 7.14e-13 GB AAA52304 "defensin precursor [Homo sapiens]" 96.67 94 100.00 100.00 2.27e-12 PIR B40499 "defensin alpha-3 precursor, neutrophil-specific [validated] - human" 96.67 94 100.00 100.00 2.27e-12 PRF 1811319A "neutrophil granule peptide HP1" 100.00 30 100.00 100.00 1.60e-11 PRF 1912193A defensin 100.00 94 100.00 100.00 7.14e-13 PRF 2115200A "neutrophil peptide" 100.00 94 100.00 100.00 7.14e-13 REF NP_001035965 "neutrophil defensin 1 isoform 2 preproprotein [Homo sapiens]" 100.00 94 100.00 100.00 7.14e-13 REF NP_001289194 "neutrophil defensin 1 isoform 1 preproprotein [Homo sapiens]" 100.00 101 100.00 100.00 6.02e-13 REF NP_004075 "neutrophil defensin 1 preproprotein [Homo sapiens]" 100.00 94 100.00 100.00 7.14e-13 REF NP_005208 "neutrophil defensin 3 preproprotein [Homo sapiens]" 96.67 94 100.00 100.00 2.27e-12 REF XP_004046640 "PREDICTED: neutrophil defensin 1-like isoform 1 [Gorilla gorilla gorilla]" 100.00 94 100.00 100.00 7.61e-13 SP P59665 "RecName: Full=Neutrophil defensin 1; AltName: Full=Defensin, alpha 1; AltName: Full=HNP-1; Short=HP-1; Short=HP1; Contains: Rec" 100.00 94 100.00 100.00 7.14e-13 SP P59666 "RecName: Full=Neutrophil defensin 3; AltName: Full=Defensin, alpha 3; AltName: Full=HNP-3; Short=HP-3; Short=HP3; Contains: Rec" 96.67 94 100.00 100.00 2.27e-12 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $HNP-1 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 $HNP-1 'recombinant technology' . Escherichia coli . pGEX-2T-Kana+GST_ProHNP-1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type microcrystal _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HNP-1 . mM . PEG400 60% w/v 'natural abundance' Cacodylate 30 mM 'natural abundance' 'Lithium Sulfate' 60 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version 2.21 loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task refinement stop_ _Details . save_ save_SPARKY _Saveframe_category software _Name SPARKY _Version 3.113 loop_ _Vendor _Address _Electronic_address Goddard . . stop_ loop_ _Task 'chemical shift assignment' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task processing stop_ _Details . save_ save_UCSF-Chimera _Saveframe_category software _Name Chimera _Version 1.3 loop_ _Vendor _Address _Electronic_address 'Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 900 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_13C-13C_DARR_40_ms,_100_ms_&_200_ms_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 13C-13C DARR 40 ms, 100 ms & 200 ms' _Sample_label $sample_1 save_ save_2D_15N-15N_PDSD_3_s_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-15N PDSD 3 s' _Sample_label $sample_1 save_ save_2D_CM5RR_0.8_ms_&_1.5_ms_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D CM5RR 0.8 ms & 1.5 ms' _Sample_label $sample_1 save_ save_2D_CHHC_200_us_&_300_us_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D CHHC 200 us & 300 us' _Sample_label $sample_1 save_ save_3D_15N-13C-13C_NCACX_5 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N-13C-13C NCACX' _Sample_label $sample_1 save_ save_3D_15N-13C-13C_NCOCX_6 _Saveframe_category NMR_applied_experiment _Experiment_name '3D 15N-13C-13C NCOCX' _Sample_label $sample_1 save_ save_2D_15N-13C_NCX_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 15N-13C NCX' _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 pH 6.5 . pH pressure 1 . atm temperature 268 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 6.5 . pH pressure 1 . atm temperature 253 . 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 C 13 'methyl carbon' ppm 0 external direct . . . 1.0 'liquid anhydrous ammonia' N 15 nitrogen ppm 0 external direct . . . 1.0 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 13C-13C DARR 40 ms, 100 ms & 200 ms' '2D CM5RR 0.8 ms & 1.5 ms' '3D 15N-13C-13C NCACX' '3D 15N-13C-13C NCOCX' '2D 15N-13C NCX' 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 HNP-1 _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 ALA C C 172.700 . 1 2 1 1 ALA CA C 51.200 . 1 3 1 1 ALA CB C 19.200 . 1 4 1 1 ALA N N 41.700 . 1 5 2 2 CYS C C 173.100 . 1 6 2 2 CYS CA C 54.900 . 1 7 2 2 CYS CB C 48.400 . 1 8 2 2 CYS N N 117.800 . 1 9 3 3 TYR C C 174.300 . 1 10 3 3 TYR CA C 56.350 . 1 11 3 3 TYR CB C 43.400 . 1 12 3 3 TYR N N 117.600 . 1 13 4 4 CYS C C 173.100 . 1 14 4 4 CYS CA C 54.350 . 1 15 4 4 CYS CB C 46.200 . 1 16 4 4 CYS N N 130.600 . 1 17 5 5 ARG C C 175.350 . 1 18 5 5 ARG CA C 55.800 . 1 19 5 5 ARG CB C 35.600 . 1 20 5 5 ARG CD C 43.150 . 1 21 5 5 ARG CG C 28.450 . 1 22 5 5 ARG CZ C 159.900 . 1 23 5 5 ARG N N 123.100 . 1 24 6 6 ILE C C 174.300 . 1 25 6 6 ILE CA C 58.150 . 1 26 6 6 ILE CB C 42.850 . 1 27 6 6 ILE CD1 C 11.800 . 1 28 6 6 ILE CG1 C 16.850 . 1 29 6 6 ILE CG2 C 29.900 . 1 30 6 6 ILE N N 122.300 . 1 31 7 7 PRO C C 174.350 . 1 32 7 7 PRO CA C 63.950 . 1 33 7 7 PRO CB C 34.600 . 1 34 7 7 PRO CD C 49.300 . 1 35 7 7 PRO CG C 24.850 . 1 36 7 7 PRO N N 134.400 . 1 37 8 8 ALA C C 174.750 . 1 38 8 8 ALA CA C 50.550 . 1 39 8 8 ALA CB C 22.200 . 1 40 8 8 ALA N N 122.600 . 1 41 9 9 CYS C C 174.700 . 1 42 9 9 CYS CA C 52.500 . 1 43 9 9 CYS CB C 35.200 . 1 44 9 9 CYS N N 115.600 . 1 45 10 10 ILE C C 175.100 . 1 46 10 10 ILE CA C 59.600 . 1 47 10 10 ILE CB C 39.200 . 1 48 10 10 ILE CD1 C 13.850 . 1 49 10 10 ILE CG1 C 17.600 . 1 50 10 10 ILE CG2 C 25.500 . 1 51 10 10 ILE N N 115.400 . 1 52 11 11 ALA C C 177.050 . 1 53 11 11 ALA CA C 53.500 . 1 54 11 11 ALA CB C 18.250 . 1 55 11 11 ALA N N 121.900 . 1 56 12 12 GLY C C 174.500 . 1 57 12 12 GLY CA C 44.250 . 1 58 12 12 GLY N N 109.600 . 1 59 13 13 GLU C C 175.300 . 1 60 13 13 GLU CA C 54.100 . 1 61 13 13 GLU CB C 33.100 . 1 62 13 13 GLU CD C 183.450 . 1 63 13 13 GLU CG C 36.100 . 1 64 13 13 GLU N N 121.300 . 1 65 14 14 ARG C C 173.100 . 1 66 14 14 ARG CA C 54.400 . 1 67 14 14 ARG N N 130.600 . 1 68 15 15 ARG C C 177.000 . 1 69 15 15 ARG CA C 56.300 . 1 70 15 15 ARG CB C 30.000 . 1 71 15 15 ARG CD C 44.150 . 1 72 15 15 ARG CG C 28.650 . 1 73 15 15 ARG CZ C 158.800 . 1 74 15 15 ARG N N 122.800 . 1 75 16 16 TYR C C 175.200 . 1 76 16 16 TYR CA C 58.000 . 1 77 16 16 TYR CB C 40.200 . 1 78 16 16 TYR CG C 133.200 . 1 79 16 16 TYR N N 128.100 . 1 80 17 17 GLY C C 173.750 . 1 81 17 17 GLY CA C 46.700 . 1 82 17 17 GLY N N 107.300 . 1 83 18 18 THR C C 173.400 . 1 84 18 18 THR CA C 61.100 . 1 85 18 18 THR CB C 71.300 . 1 86 18 18 THR CG2 C 23.400 . . 87 18 18 THR N N 124.200 . 1 88 19 19 CYS C C 173.400 . 1 89 19 19 CYS CA C 53.250 . 1 90 19 19 CYS CB C 44.750 . 1 91 19 19 CYS N N 122.300 . 1 92 20 20 ILE C C 175.200 . 1 93 20 20 ILE CA C 61.350 . 1 94 20 20 ILE CB C 37.600 . 1 95 20 20 ILE CD1 C 13.100 . 1 96 20 20 ILE CG1 C 17.800 . 1 97 20 20 ILE CG2 C 26.150 . 1 98 20 20 ILE N N 123.600 . 1 99 21 21 TYR C C 174.300 . 1 100 21 21 TYR CA C 56.700 . 1 101 21 21 TYR CB C 39.450 . 1 102 21 21 TYR CG C 128.500 . 1 103 21 21 TYR N N 125.500 . 1 104 22 22 GLN C C 175.450 . 1 105 22 22 GLN CA C 55.850 . 1 106 22 22 GLN CB C 25.550 . 1 107 22 22 GLN CD C 178.200 . 1 108 22 22 GLN CG C 33.600 . 1 109 22 22 GLN N N 129.000 . 1 110 23 23 GLY C C 172.000 . 1 111 23 23 GLY CA C 45.700 . 1 112 23 23 GLY N N 103.400 . 1 113 24 24 ARG C C 173.700 . 1 114 24 24 ARG CA C 53.400 . 1 115 24 24 ARG CB C 34.100 . 1 116 24 24 ARG CD C 42.900 . 1 117 24 24 ARG CG C 27.200 . 1 118 24 24 ARG N N 118.400 . 1 119 25 25 LEU C C 176.100 . 1 120 25 25 LEU CA C 53.350 . 1 121 25 25 LEU CB C 42.900 . 1 122 25 25 LEU CD1 C 25.000 . 2 123 25 25 LEU CD2 C 24.100 . 2 124 25 25 LEU CG C 27.100 . 1 125 25 25 LEU N N 120.200 . 1 126 26 26 TRP C C 177.000 . 1 127 26 26 TRP CA C 53.750 . 1 128 26 26 TRP CB C 30.700 . 1 129 26 26 TRP N N 120.700 . 1 130 27 27 ALA C C 174.700 . 1 131 27 27 ALA CA C 52.850 . 1 132 27 27 ALA CB C 18.600 . 1 133 27 27 ALA N N 127.100 . 1 134 28 28 PHE CA C 58.350 . 1 135 28 28 PHE CB C 41.550 . 1 136 28 28 PHE CG C 130.900 . 1 137 28 28 PHE N N 123.800 . 1 138 29 29 CYS C C 174.400 . 1 139 29 29 CYS CA C 54.650 . 1 140 29 29 CYS CB C 40.450 . 1 141 29 29 CYS N N 121.900 . 1 142 30 30 CYS C C 179.200 . 1 143 30 30 CYS CA C 57.000 . 1 144 30 30 CYS CB C 48.600 . 1 145 30 30 CYS N N 121.100 . 1 stop_ save_