data_5264 #Corrected using PDB structure: 1KJ6A # #N.B. (Observed* = Observed shift + Offset correction) # #After reference correction, the following residues still #have a HA chemical shift difference (obs*-pred) greater than 0.7ppm: #NUM AA CS Observed* Predicted # 41 C HA 5.54 6.30 # #After reference correction, the following residues still #have a HN chemical shift difference (obs*-pred) greater than 2.0ppm: #NUM AA CS Observed* Predicted # 17 R H 8.63 5.84 # #The average CS difference between predicted and observed: #HA CA CB CO N HN #0.07 N/A N/A N/A N/A -0.22 # #bmr5264.str.corr chemical shifts have been re-referenced with the following #offsets (these values have been added to the original bmr5264.str file): #HA CA CB CO N HN #N/A N/A N/A N/A N/A N/A # #The 95% confidence intervals for the above recommended offsets are: # HA CA CB CO N HN #+/-0.04 N/A N/A N/A N/A +/-0.10 # #The Correlation Coefficients between predicted and observed #chemical shifts are: #HA CA CB CO N HN #0.846 N/A N/A N/A N/A 0.332 # #The RMSD between predicted and observed* (reference #corrected) chemical shifts are: #HA CA CB CO N HN #0.138 N/A N/A N/A N/A 0.335 # ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of Human beta-Defensin 3 ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schibli D. J. . 2 Hunter H. N. . 3 Aseyev V. . . 4 Starner T. D. . 5 Wiencek J. M. . 6 McCray P. M. Jr. 7 Tack B. F. . 8 Vogel H. J. . stop_ _BMRB_accession_number 5264 _BMRB_flat_file_name bmr5264.str _Entry_type new _Submission_date 2002-01-23 _Accession_date 2002-01-24 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count '1H chemical shifts' 241 stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; The Solution Structures of the Human beta-Defensins lead to a Better Understanding of the Potent Bactericidal Activity of HBD3 against Staphylococcus aureus ; _Citation_status published _Citation_type journal _MEDLINE_UI_code 21864161 _PubMed_ID 11741980 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schibli D. J. . 2 Hunter H. N. . 3 Aseyev V. . . 4 Starner T. D. . 5 Wiencek J. M. . 6 McCray P. M. Jr. 7 Tack B. F. . 8 Vogel H. J. . stop_ _Journal_abbreviation "J. Biol. Chem." _Journal_volume 277 _Journal_issue 10 _Page_first 8279 _Page_last 8289 _Year 2002 loop_ _Keyword "defensin" "antimicrobial protein" "human beta-defensin 3" "beta-defensin" "HBD3" stop_ save_ ################################## # Molecular system description # ################################## save_system_HBD-3 _Saveframe_category molecular_system _Mol_system_name "Human Beta-defensin 3" _Abbreviation_common HBD-3 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label "Beta-defensin 3" $HBD-3 stop_ _System_physical_state native _System_oligomer_state dimer _System_paramagnetic no _System_thiol_state 'all disulfide bound' loop_ _Biological_function "antimicrobial protein" stop_ loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Database_entry_details PDB 1KJ6 ? . stop_ save_ ######################## # Monomeric polymers # ######################## save_HBD-3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common "Human beta-defensin 3" _Name_variant . _Abbreviation_common HBD-3 _Molecular_mass 5168.9 _Mol_thiol_state 'all disulfide bound' ############################## # Polymer residue sequence # ############################## _Residue_count 45 _Mol_residue_sequence ; GIINTLQKYYCRVRGGRCAV LSCLPKEEQIGKCSTRGRKC CRRKK ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 ILE 4 ASN 5 THR 6 LEU 7 GLN 8 LYS 9 TYR 10 TYR 11 CYS 12 ARG 13 VAL 14 ARG 15 GLY 16 GLY 17 ARG 18 CYS 19 ALA 20 VAL 21 LEU 22 SER 23 CYS 24 LEU 25 PRO 26 LYS 27 GLU 28 GLU 29 GLN 30 ILE 31 GLY 32 LYS 33 CYS 34 SER 35 THR 36 ARG 37 GLY 38 ARG 39 LYS 40 CYS 41 CYS 42 ARG 43 ARG 44 LYS 45 LYS stop_ _Sequence_homology_query_date 2004-07-29 _Sequence_homology_query_revised_last_date 2004-07-16 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 1KJ6 "A Chain A, Solution Structure Of HumanBeta-Defensin 3" 100.00 45 100 100 6e-21 DBJ BAB40572.1 "defensin like protein [Homo sapiens]" 67.16 67 100 100 6e-21 EMBL CAC03097.1 "beta-defensin-3 [Homo sapiens]" 67.16 67 100 100 6e-21 GenBank AAK61549.1 "beta-defensin-3 [Pan troglodytes]" 70.31 64 98 100 7e-19 GenBank AAF73853.1 "beta defensin-3 [Homo sapiens]" 67.16 67 100 100 6e-21 GenBank AAG02237.1 "beta-defensin 3 [Homo sapiens]" 67.16 67 100 100 6e-21 GenBank AAG22030.1 "beta-defensin 3 [Homo sapiens]" 67.16 67 100 100 6e-21 GenBank AAM62424.1 "beta-defensin-3 [Homo sapiens]" 67.16 67 98 98 2e-19 REF NP_061131.1 "defensin, beta 103A, precursor; betadefensin-3; defensin, beta 3 [Homo sapiens]" 67.16 67 100 100 6e-21 SWISS-PROT Q95JD2 "D103_PANTR Beta-defensin 103 precursor(Beta-defensin 3) (DEFB-3) (BD-3)" 70.31 64 98 100 7e-19 SWISS-PROT P81534 "D103_HUMAN Beta-defensin 103 precursor(Beta-defensin 3) (DEFB-3) (BD-3) (hBD-3) (HBD3)(Defensin like protein)" 67.16 67 100 100 6e-21 tpg DAA01350.1 "TPA: DEFB103-like protein [Papioanubis]" 67.16 67 100 100 6e-21 stop_ save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bonds _Saveframe_category crosslink_bonds loop_ _Bond_order _Bond_type _Atom_one_mol_system_component_name _Atom_one_residue_seq_code _Atom_one_residue_label _Atom_one_atom_name _Atom_two_mol_system_component_name _Atom_two_residue_seq_code _Atom_two_residue_label _Atom_two_atom_name single disulfide "Beta-defensin 3" 11 CYS SG "Beta-defensin 3" 40 CYS SG single disulfide "Beta-defensin 3" 18 CYS SG "Beta-defensin 3" 33 CYS SG single disulfide "Beta-defensin 3" 23 CYS SG "Beta-defensin 3" 41 CYS SG stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Organ _Tissue $HBD-3 Human 9606 Eukaryota Metazoa Homo sapiens heart "skeletal muscle; placenta; esophagus; trachea; oral mucosa; skin tissues" 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 _Details $HBD-3 'recombinant technology' . . . . . ; Produced by Peprotech (Rocky Hill, NJ). ; stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HBD-3 0.36 mM . D2O 10 % . H2O 90 % . stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $HBD-3 0.36 mM . D2O 100 % . stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 2.6 loop_ _Task collection stop_ _Details Bruker save_ save_NMRPipe _Saveframe_category software _Name NMRPipe _Version 1.8 loop_ _Task processing stop_ _Details ; Delaglio, G., Grzejiek, S., Vuister, G., Zhu, G., Pfeifer, J., Bax, A. ; save_ save_NMRView _Saveframe_category software _Name NMRView _Version 4.1.3 loop_ _Task "data analysis" stop_ _Details ; Johnson, B.A., Blevins, R.A. ; save_ save_CNS _Saveframe_category software _Name CNS _Version 1.0 loop_ _Task refinement stop_ _Details ; A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren. ; save_ save_Aria _Saveframe_category software _Name Aria _Version 1.0 loop_ _Task refinement stop_ _Details "J.Linge, S.O'Donoghue, M.Nilges." save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model AVANCE _Field_strength 500 save_ save_NMR_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 800 save_ ############################# # NMR applied experiments # ############################# save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name ; 2D NOESY 2D TOCSY 2D DQF-COSY ; _Details ; A cryo-probe was used on the Bruker spectrometer. ; save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 4.00 0.1 n/a temperature 298 0.1 K pressure 1 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Saveframe_category chemical_shift_reference 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 0.0 internal direct . . . 1.0 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # Index Value Definition # # # # 1 Unique # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups # # 3 Aromatic atoms on opposite sides of the ring # # (e.g. Tyr HE1 and HE2 protons) # # 4 Intraresidue ambiguities (e.g. Lys HG and # # HD protons) # # 5 Interresidue ambiguities (Lys 12 vs. Lys 27) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name "Beta-defensin 3" loop_ _Atom_shift_assign_ID _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 GLY HA3 H 3.87 . 2 2 2 ILE H H 8.53 . 1 3 2 ILE HA H 4.23 . 1 4 2 ILE HB H 1.84 . 1 5 2 ILE HG13 H 1.47 . 9 6 2 ILE HG12 H 1.20 . 9 7 2 ILE HD1 H 0.88 . 1 8 2 ILE HG2 H 0.91 . 4 9 3 ILE H H 8.36 . 1 10 3 ILE HA H 4.18 . 1 11 3 ILE HB H 1.87 . 1 12 3 ILE HG13 H 1.51 . 9 13 3 ILE HG12 H 1.22 . 9 14 3 ILE HD1 H 0.86 . 1 15 3 ILE HG2 H 0.85 . 4 16 4 ASN H H 8.60 . 1 17 4 ASN HA H 4.77 . 1 18 4 ASN HB3 H 2.83 . 2 19 4 ASN HD21 H 6.92 . 2 20 4 ASN HD22 H 7.64 . 2 21 5 THR H H 8.17 . 1 22 5 THR HA H 4.23 . 1 23 5 THR HB H 4.29 . 1 24 5 THR HG2 H 1.21 . 1 25 6 LEU H H 8.20 . 1 26 6 LEU HA H 4.33 . 1 27 6 LEU HB3 H 1.72 . 2 28 6 LEU HG H 1.62 . 1 29 6 LEU HD1 H 0.92 . 2 30 6 LEU HD2 H 0.85 . 2 31 7 GLN H H 8.17 . 1 32 7 GLN HA H 4.13 . 1 33 7 GLN HB3 H 2.08 . 2 34 7 GLN HB2 H 1.94 . 2 35 7 GLN HG3 H 2.33 . 2 36 7 GLN HE21 H 6.74 . 2 37 7 GLN HE22 H 7.44 . 2 38 8 LYS H H 8.16 . 1 39 8 LYS HA H 4.04 . 1 40 8 LYS HB3 H 1.71 . 2 41 8 LYS HG3 H 1.29 . 2 42 8 LYS HG2 H 1.19 . 2 43 8 LYS HD2 H 1.61 . 2 44 8 LYS HE2 H 2.92 . 2 45 9 TYR H H 7.99 . 1 46 9 TYR HA H 4.53 . 1 47 9 TYR HB3 H 2.99 . 2 48 9 TYR HB2 H 3.16 . 2 49 9 TYR HD1 H 6.98 . 2 50 9 TYR HE1 H 6.76 . 2 51 10 TYR H H 8.07 . 1 52 10 TYR HA H 4.29 . 1 53 10 TYR HB3 H 3.08 . 2 54 10 TYR HD1 H 7.10 . 2 55 10 TYR HE1 H 6.82 . 2 56 11 CYS H H 8.34 . 1 57 11 CYS HA H 4.25 . 1 58 11 CYS HB3 H 3.09 . 2 59 11 CYS HB2 H 2.97 . 2 60 12 ARG H H 7.96 . 1 61 12 ARG HA H 4.27 . 1 62 12 ARG HB3 H 1.95 . 2 63 12 ARG HG3 H 1.69 . 2 64 12 ARG HD3 H 3.21 . 2 65 12 ARG HE H 7.21 . 1 66 13 VAL H H 8.30 . 1 67 13 VAL HA H 3.90 . 1 68 13 VAL HB H 2.13 . 1 69 13 VAL HG2 H 0.92 . 2 70 13 VAL HG1 H 0.95 . 2 71 14 ARG H H 7.31 . 1 72 14 ARG HA H 4.30 . 1 73 14 ARG HB3 H 2.12 . 2 74 14 ARG HB2 H 1.94 . 2 75 14 ARG HG3 H 1.64 . 2 76 14 ARG HG2 H 1.53 . 2 77 14 ARG HD3 H 2.98 . 2 78 14 ARG HE H 6.88 . 1 79 15 GLY H H 8.01 . 1 80 15 GLY HA3 H 3.85 . 2 81 15 GLY HA2 H 4.22 . 2 82 16 GLY H H 8.18 . 1 83 16 GLY HA3 H 4.57 . 2 84 16 GLY HA2 H 3.31 . 2 85 17 ARG H H 8.84 . 1 86 17 ARG HA H 4.68 . 1 87 17 ARG HB3 H 1.74 . 2 88 17 ARG HB2 H 1.68 . 2 89 17 ARG HG3 H 1.53 . 2 90 17 ARG HG2 H 1.26 . 2 91 17 ARG HD3 H 3.18 . 2 92 17 ARG HD2 H 3.00 . 2 93 17 ARG HE H 9.22 . 1 94 17 ARG HH21 H 6.85 . 9 95 18 CYS H H 8.92 . 1 96 18 CYS HA H 5.36 . 1 97 18 CYS HB3 H 2.94 . 2 98 18 CYS HB2 H 2.72 . 2 99 19 ALA H H 9.37 . 1 100 19 ALA HA H 4.54 . 1 101 19 ALA HB H 1.32 . 1 102 20 VAL H H 8.64 . 1 103 20 VAL HA H 3.85 . 1 104 20 VAL HB H 2.03 . 1 105 20 VAL HG2 H 0.97 . 2 106 20 VAL HG1 H 1.01 . 2 107 21 LEU H H 8.35 . 1 108 21 LEU HA H 4.41 . 1 109 21 LEU HB3 H 1.72 . 2 110 21 LEU HG H 1.56 . 1 111 21 LEU HD1 H 0.95 . 2 112 21 LEU HD2 H 0.93 . 2 113 22 SER H H 8.19 . 1 114 22 SER HA H 4.48 . 1 115 22 SER HB3 H 3.79 . 2 116 22 SER HB2 H 3.88 . 2 117 23 CYS H H 8.58 . 1 118 23 CYS HA H 4.78 . 1 119 23 CYS HB3 H 3.40 . 2 120 23 CYS HB2 H 2.66 . 2 121 24 LEU H H 9.24 . 1 122 24 LEU HA H 4.50 . 1 123 24 LEU HB3 H 1.77 . 2 124 24 LEU HB2 H 1.30 . 2 125 24 LEU HG H 1.63 . 1 126 24 LEU HD1 H 0.96 . 4 127 24 LEU HD2 H 0.87 . 4 128 25 PRO HA H 4.35 . 1 129 25 PRO HB3 H 1.87 . 2 130 25 PRO HB2 H 2.43 . 2 131 25 PRO HG3 H 2.16 . 2 132 25 PRO HG2 H 2.06 . 2 133 25 PRO HD3 H 3.75 . 2 134 25 PRO HD2 H 3.82 . 2 135 26 LYS H H 7.83 . 1 136 26 LYS HA H 4.35 . 1 137 26 LYS HB3 H 1.87 . 2 138 26 LYS HB2 H 2.11 . 2 139 26 LYS HG3 H 1.42 . 2 140 26 LYS HD2 H 1.77 . 2 141 26 LYS HE2 H 2.98 . 2 142 27 GLU H H 8.12 . 1 143 27 GLU HA H 4.86 . 1 144 27 GLU HB3 H 1.82 . 2 145 27 GLU HB2 H 1.65 . 2 146 27 GLU HG3 H 2.52 . 2 147 27 GLU HG2 H 2.12 . 2 148 28 GLU H H 9.03 . 1 149 28 GLU HA H 4.75 . 1 150 28 GLU HB3 H 1.97 . 2 151 28 GLU HB2 H 1.87 . 2 152 28 GLU HG3 H 2.19 . 2 153 28 GLU HG2 H 2.12 . 2 154 29 GLN H H 9.03 . 1 155 29 GLN HA H 4.99 . 1 156 29 GLN HB3 H 2.09 . 2 157 29 GLN HG3 H 2.48 . 2 158 29 GLN HE21 H 7.10 . 2 159 29 GLN HE22 H 7.19 . 2 160 30 ILE H H 8.74 . 1 161 30 ILE HA H 4.72 . 1 162 30 ILE HB H 2.10 . 1 163 30 ILE HG13 H 0.97 . 1 164 30 ILE HD1 H 0.67 . 1 165 30 ILE HG2 H 0.82 . 4 166 31 GLY H H 7.63 . 1 167 31 GLY HA3 H 4.34 . 2 168 31 GLY HA2 H 4.05 . 2 169 32 LYS H H 8.95 . 1 170 32 LYS HA H 4.93 . 1 171 32 LYS HB3 H 1.97 . 2 172 32 LYS HG3 H 1.38 . 2 173 32 LYS HD2 H 1.67 . 2 174 32 LYS HE2 H 2.95 . 2 175 33 CYS H H 8.42 . 1 176 33 CYS HA H 4.84 . 1 177 33 CYS HB3 H 3.29 . 2 178 34 SER H H 8.20 . 1 179 34 SER HA H 4.36 . 1 180 34 SER HB3 H 3.90 . 2 181 34 SER HB2 H 4.08 . 2 182 35 THR H H 8.04 . 1 183 35 THR HA H 4.27 . 1 184 35 THR HB H 4.15 . 1 185 35 THR HG2 H 1.27 . 1 186 36 ARG H H 8.46 . 1 187 36 ARG HA H 4.21 . 1 188 36 ARG HB3 H 1.77 . 2 189 36 ARG HB2 H 1.99 . 2 190 36 ARG HG3 H 1.65 . 2 191 36 ARG HD3 H 3.21 . 2 192 37 GLY H H 8.17 . 1 193 37 GLY HA3 H 4.11 . 2 194 37 GLY HA2 H 3.78 . 2 195 38 ARG H H 7.62 . 1 196 38 ARG HA H 4.57 . 1 197 38 ARG HB3 H 1.76 . 2 198 38 ARG HG3 H 1.60 . 2 199 38 ARG HD3 H 3.02 . 2 200 38 ARG HE H 7.12 . 1 201 39 LYS H H 8.97 . 1 202 39 LYS HA H 4.32 . 1 203 39 LYS HB3 H 1.56 . 2 204 39 LYS HG3 H 1.35 . 2 205 39 LYS HD2 H 1.55 . 2 206 39 LYS HE2 H 3.04 . 2 207 40 CYS H H 8.31 . 1 208 40 CYS HA H 5.23 . 1 209 40 CYS HB3 H 2.49 . 2 210 40 CYS HB2 H 2.55 . 2 211 41 CYS H H 9.45 . 1 212 41 CYS HA H 5.47 . 1 213 41 CYS HB3 H 2.84 . 2 214 41 CYS HB2 H 2.55 . 2 215 42 ARG H H 9.43 . 1 216 42 ARG HA H 4.92 . 1 217 42 ARG HB3 H 1.92 . 2 218 42 ARG HB2 H 1.39 . 2 219 42 ARG HG3 H 1.80 . 2 220 42 ARG HD3 H 3.38 . 2 221 42 ARG HD2 H 2.94 . 2 222 42 ARG HE H 7.66 . 1 223 43 ARG H H 8.99 . 1 224 43 ARG HA H 4.24 . 1 225 43 ARG HB3 H 1.90 . 2 226 43 ARG HG3 H 1.74 . 2 227 43 ARG HD3 H 3.25 . 2 228 43 ARG HE H 7.35 . 1 229 44 LYS H H 8.60 . 1 230 44 LYS HA H 4.20 . 1 231 44 LYS HB3 H 1.83 . 2 232 44 LYS HG3 H 1.37 . 2 233 44 LYS HG2 H 1.31 . 2 234 44 LYS HD2 H 1.61 . 2 235 44 LYS HE2 H 2.93 . 2 236 45 LYS H H 8.24 . 1 237 45 LYS HA H 4.10 . 1 238 45 LYS HB3 H 1.78 . 2 239 45 LYS HG3 H 1.43 . 2 240 45 LYS HD2 H 1.71 . 2 241 45 LYS HE2 H 3.01 . 2 stop_ loop_ _Atom_shift_assign_ID_ambiguity 8 15 126,127 165 stop_ save_