data_4642 #Corrected using PDB structure: 1FD3D # #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 # 3 G HA 3.46 4.39 # 18 V HA 3.25 4.21 # #The average CS difference between predicted and observed: #HA CA CB CO N HN #0.11 N/A N/A N/A N/A 0.06 # #bmr4642.str.corr chemical shifts have been re-referenced with the following #offsets (these values have been added to the original bmr4642.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 #+/-0.05 N/A N/A N/A N/A +/-0.11 # #The Correlation Coefficients between predicted and observed #chemical shifts are: #HA CA CB CO N HN #0.770 N/A N/A N/A N/A 0.686 # #The RMSD between predicted and observed* (reference #corrected) chemical shifts are: #HA CA CB CO N HN #0.163 N/A N/A N/A N/A 0.319 # ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; SOLUTION STRUCTURE OF HUMAN BETA-DEFENSIN-2 ; loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sawai M. V. . 2 Jia H. P. . 3 Liu L. . . 4 Aseyev V. . . 5 Wiencek J. M. . 6 McCray P. B. Jr. 7 Ganz T. . . 8 Kearney W. R. . 9 Tack B. F. . stop_ _BMRB_accession_number 4642 _BMRB_flat_file_name bmr4642.str _Entry_type new _Submission_date 2000-09-06 _Accession_date 2001-03-16 _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' 245 stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_title ; The NMR Structure of Human Beta-Defensin-2 Reveals a Novel Alpha-Helical Segment ; _Citation_status published _Citation_type Journal _MEDLINE_UI_code . _PubMed_ID 11300761 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Sawai M. V. . 2 Jia H. P. . 3 Liu L. . . 4 Aseyev V. . . 5 Wiencek J. M. . 6 McCray P. B. Jr. 7 Ganz T. . . 8 Kearney W. R. . 9 Tack B. F. . stop_ _Journal_abbreviation Biochemistry _Journal_name_full ? _Journal_volume 40 _Page_first 3810 _Page_last 3816 _Year 2001 loop_ _Keyword DEFENSIN "SOLUTION STRUCTURE" stop_ save_ ################################## # Molecular system description # ################################## save_system_Human_beta_defensin_2 _Saveframe_category molecular_system _Mol_system_name "HUMAN BETA-DEFENSIN-2" _Abbreviation_common "HUMAN BETA-DEFENSIN-2" loop_ _Mol_system_component_name _Mol_label "BETA-DEFENSIN-2" $Human_beta_defensin_2 stop_ _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Database_entry_details PDB 1FQQ ? . stop_ save_ ######################## # Monomeric polymers # ######################## save_Human_beta_defensin_2 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common "HUMAN BETA-DEFENSIN-2" _Name_variant . _Abbreviation_common "HUMAN BETA-DEFENSIN-2" _Mol_thiol_state 'all disulfide bound' ############################## # Polymer residue sequence # ############################## _Residue_count 41 _Mol_residue_sequence ; GIGDPVTCLKSGAICHPVFC PRRYKQIGTCGLPGTKCCKK P ; loop_ _Residue_seq_code _Residue_label 1 GLY 2 ILE 3 GLY 4 ASP 5 PRO 6 VAL 7 THR 8 CYS 9 LEU 10 LYS 11 SER 12 GLY 13 ALA 14 ILE 15 CYS 16 HIS 17 PRO 18 VAL 19 PHE 20 CYS 21 PRO 22 ARG 23 ARG 24 TYR 25 LYS 26 GLN 27 ILE 28 GLY 29 THR 30 CYS 31 GLY 32 LEU 33 PRO 34 GLY 35 THR 36 LYS 37 CYS 38 CYS 39 LYS 40 LYS 41 PRO 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 1E4Q "A Chain A, Solution Structure Of The HumanDefensin Hbd-2" 110.81 37 100 100 9e-17 PDB 1FD3 "A Chain A, Human Beta-Defensin 2" 100.00 41 100 100 4e-20 PDB 1FD4 "A Chain A, Human Beta-Defensin 2" 100.00 41 100 100 4e-20 PDB 1FQQ "A Chain A, Solution Structure Of HumanBeta-Defensin-2" 100.00 41 100 100 2e-19 EMBL CAA95992.1 "skin-antimicrobial peptide 1 (SAP1)[Homo sapiens]" 64.06 64 100 100 4e-20 EMBL CAB65126.1 "beta-defensin-2 [Homo sapiens]" 64.06 64 100 100 4e-20 GenBank AAL50683.1 "human beta-defensin-2 precursor[synthetic construct]" 97.62 42 100 100 4e-20 GenBank AAC33549.1 "beta-defensin 2 [Homo sapiens]" 64.06 64 100 100 4e-20 GenBank AAC69554.1 "beta defensin 2; HBD-2 [Homo sapiens]" 64.06 64 100 100 4e-20 GenBank AAH69285.1 "Defensin, beta 4,, precursor [Homosapiens]" 64.06 64 100 100 4e-20 GenBank AAN64161.1 "human beta-defensin-2 precursor[synthetic construct]" 60.29 68 100 100 4e-20 REF NP_004933.1 "defensin, beta 4, precursor;skin-antimicrobial peptide 1; defensin, beta 2 [Homosapiens]" 64.06 64 100 100 4e-20 SWISS-PROT O15263 "BD02_HUMAN Beta-defensin 2 precursor (BD-2)(hBD-2) (Defensin, beta 2) (Skin-antimicrobial peptide1) (SAP1)" 64.06 64 100 100 4e-20 SWISS-PROT Q9BDS9 "BD02_MACMU Beta-defensin 2 precursor (BD-2)(RhBD-2) (Defensin, beta 2)" 64.06 64 98 100 9e-20 SWISS-PROT Q9TT12 "BD02_PANTR Beta-defensin 2 precursor (BD-2)(Defensin, beta 2)" 64.06 64 98 98 2e-19 stop_ save_ ######################################## # Molecular bond linkage definitions # ######################################## save_crosslink_bond_definitions _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-2" 8 CYS SG "BETA-DEFENSIN-2" 37 CYS SG single disulfide "BETA-DEFENSIN-2" 15 CYS SG "BETA-DEFENSIN-2" 30 CYS SG single disulfide "BETA-DEFENSIN-2" 20 CYS SG "BETA-DEFENSIN-2" 38 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 $Human_beta_defensin_2 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 $Human_beta_defensin_2 ? . . . . . 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 $Human_beta_defensin_2 0.87 mM . "sodium phosphate buffer" 45 mM . H2O 90 % . D2O 10 % . stop_ save_ ############################ # Computer software used # ############################ save_DYANA _Saveframe_category software _Name DYANA _Version 1.5 loop_ _Task "structure solution" stop_ _Details Guentert save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Varian _Model INOVA _Field_strength 500 save_ ############################# # NMR applied experiments # ############################# save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Details ; 2D NOESY DOF-COSY TOCSY ; save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.74 . n/a temperature 298 . K 'ionic strength' 0.045 . M pressure 1.013 . atm stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_ref_1 _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 . H 1 . ppm . . . . . . . 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_ref_1 _Mol_system_component_name "BETA-DEFENSIN-2" 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 HA2 H 3.78 . 2 2 1 GLY HA3 H 3.72 . 2 3 2 ILE H H 8.57 . 1 4 2 ILE HA H 3.90 . 1 5 2 ILE HB H 1.60 . 1 6 2 ILE HG2 H 0.91 . 1 7 2 ILE HG12 H 1.50 . 2 8 2 ILE HG13 H 0.85 . 2 9 2 ILE HD1 H 0.70 . 1 10 3 GLY H H 9.27 . 1 11 3 GLY HA2 H 3.35 . 1 12 3 GLY HA3 H 3.35 . 1 13 4 ASP H H 7.27 . 1 14 4 ASP HA H 4.61 . 1 15 4 ASP HB2 H 2.81 . 2 16 4 ASP HB3 H 2.51 . 2 17 5 PRO HA H 4.09 . 1 18 5 PRO HB2 H 2.42 . 1 19 5 PRO HB3 H 2.42 . 1 20 5 PRO HG2 H 2.10 . 1 21 5 PRO HG3 H 2.10 . 1 22 5 PRO HD2 H 3.82 . 2 23 5 PRO HD3 H 3.62 . 2 24 6 VAL H H 7.67 . 1 25 6 VAL HA H 3.54 . 1 26 6 VAL HB H 2.03 . 1 27 6 VAL HG1 H 0.92 . 2 28 6 VAL HG2 H 0.82 . 2 29 7 THR H H 8.84 . 1 30 7 THR HA H 3.62 . 1 31 7 THR HB H 3.78 . 1 32 7 THR HG2 H 1.16 . 1 33 8 CYS H H 7.50 . 1 34 8 CYS HA H 3.90 . 1 35 8 CYS HB2 H 2.79 . 1 36 8 CYS HB3 H 2.79 . 1 37 9 LEU H H 7.83 . 1 38 9 LEU HA H 4.28 . 1 39 9 LEU HB2 H 1.69 . 2 40 9 LEU HB3 H 1.64 . 2 41 9 LEU HG H 1.79 . 1 42 9 LEU HD1 H 0.85 . 1 43 9 LEU HD2 H 0.85 . 1 44 10 LYS H H 8.30 . 1 45 10 LYS HA H 4.05 . 1 46 10 LYS HB2 H 1.83 . 2 47 10 LYS HB3 H 1.72 . 2 48 10 LYS HG2 H 1.41 . 1 49 10 LYS HG3 H 1.41 . 1 50 10 LYS HD2 H 1.53 . 1 51 10 LYS HD3 H 1.53 . 1 52 10 LYS HE2 H 2.81 . 1 53 10 LYS HE3 H 2.81 . 1 54 10 LYS HZ H 7.42 . 5 55 11 SER H H 7.50 . 1 56 11 SER HA H 4.44 . 1 57 11 SER HB2 H 3.89 . 1 58 11 SER HB3 H 3.89 . 1 59 12 GLY H H 7.97 . 1 60 12 GLY HA2 H 3.93 . 2 61 12 GLY HA3 H 3.75 . 2 62 13 ALA H H 7.02 . 1 63 13 ALA HA H 4.80 . 1 64 13 ALA HB H 1.15 . 1 65 14 ILE H H 8.37 . 1 66 14 ILE HA H 4.64 . 1 67 14 ILE HB H 1.78 . 1 68 14 ILE HG2 H 0.85 . 1 69 14 ILE HG12 H 1.13 . 2 70 14 ILE HG13 H 1.03 . 2 71 14 ILE HD1 H 0.51 . 1 72 15 CYS H H 8.48 . 1 73 15 CYS HA H 5.50 . 1 74 15 CYS HB2 H 2.72 . 2 75 15 CYS HB3 H 2.68 . 2 76 16 HIS H H 9.58 . 1 77 16 HIS HA H 4.83 . 1 78 16 HIS HB2 H 3.08 . 2 79 16 HIS HB3 H 2.42 . 2 80 16 HIS HD2 H 7.25 . 1 81 16 HIS HE1 H 7.16 . 1 82 17 PRO HA H 4.36 . 1 83 17 PRO HB2 H 2.16 . 1 84 17 PRO HB3 H 2.16 . 1 85 17 PRO HG2 H 1.72 . 2 86 17 PRO HG3 H 1.67 . 2 87 17 PRO HD2 H 3.41 . 2 88 17 PRO HD3 H 2.34 . 2 89 18 VAL H H 8.72 . 1 90 18 VAL HA H 3.14 . 1 91 18 VAL HB H 2.49 . 1 92 18 VAL HG1 H 0.89 . 2 93 18 VAL HG2 H 0.81 . 2 94 19 PHE H H 9.27 . 1 95 19 PHE HA H 4.80 . 1 96 19 PHE HB2 H 2.94 . 1 97 19 PHE HB3 H 2.94 . 1 98 19 PHE HD1 H 6.91 . 1 99 19 PHE HD2 H 6.91 . 1 100 19 PHE HE1 H 7.16 . 1 101 19 PHE HE2 H 7.16 . 1 102 19 PHE HZ H 7.25 . 1 103 20 CYS H H 8.87 . 1 104 20 CYS HA H 4.96 . 1 105 20 CYS HB2 H 2.66 . 1 106 20 CYS HB3 H 2.66 . 1 107 21 PRO HA H 4.17 . 1 108 21 PRO HB2 H 1.98 . 2 109 21 PRO HB3 H 1.27 . 2 110 21 PRO HG2 H 0.90 . 2 111 21 PRO HG3 H 0.85 . 2 112 21 PRO HD2 H 2.70 . 2 113 21 PRO HD3 H 2.40 . 2 114 22 ARG H H 8.30 . 1 115 22 ARG HA H 3.91 . 1 116 22 ARG HB2 H 1.67 . 1 117 22 ARG HB3 H 1.67 . 1 118 22 ARG HG2 H 1.62 . 2 119 22 ARG HG3 H 1.58 . 2 120 22 ARG HD2 H 3.11 . 1 121 22 ARG HD3 H 3.11 . 1 122 22 ARG HE H 7.15 . 1 123 23 ARG H H 8.53 . 1 124 23 ARG HA H 3.73 . 1 125 23 ARG HB2 H 2.25 . 1 126 23 ARG HB3 H 2.25 . 1 127 23 ARG HG2 H 1.83 . 2 128 23 ARG HG3 H 1.49 . 2 129 23 ARG HD2 H 3.09 . 1 130 23 ARG HD3 H 3.09 . 1 131 23 ARG HE H 7.04 . 1 132 24 TYR H H 8.32 . 1 133 24 TYR HA H 4.55 . 1 134 24 TYR HB2 H 3.20 . 2 135 24 TYR HB3 H 2.25 . 2 136 24 TYR HD1 H 6.75 . 1 137 24 TYR HD2 H 6.75 . 1 138 24 TYR HE1 H 6.61 . 1 139 24 TYR HE2 H 6.61 . 1 140 25 LYS H H 8.43 . 1 141 25 LYS HA H 4.45 . 1 142 25 LYS HB2 H 1.63 . 1 143 25 LYS HB3 H 1.63 . 1 144 25 LYS HG2 H 1.29 . 2 145 25 LYS HG3 H 1.20 . 2 146 25 LYS HD2 H 1.51 . 1 147 25 LYS HD3 H 1.51 . 1 148 25 LYS HE2 H 2.82 . 1 149 25 LYS HE3 H 2.82 . 1 150 26 GLN H H 9.03 . 1 151 26 GLN HA H 4.73 . 1 152 26 GLN HB2 H 1.98 . 1 153 26 GLN HB3 H 1.98 . 1 154 26 GLN HG2 H 2.36 . 1 155 26 GLN HG3 H 2.36 . 1 156 26 GLN HE21 H 7.90 . 2 157 26 GLN HE22 H 7.26 . 2 158 27 ILE H H 8.69 . 1 159 27 ILE HA H 4.68 . 1 160 27 ILE HB H 2.09 . 1 161 27 ILE HG2 H 0.76 . 1 162 27 ILE HG12 H 0.65 . 2 163 27 ILE HG13 H 0.61 . 2 164 27 ILE HD1 H 0.68 . 1 165 28 GLY H H 7.38 . 1 166 28 GLY HA2 H 4.11 . 2 167 28 GLY HA3 H 4.55 . 2 168 29 THR H H 8.74 . 1 169 29 THR HA H 4.80 . 1 170 29 THR HB H 4.37 . 1 171 29 THR HG2 H 1.06 . 1 172 30 CYS H H 7.25 . 1 173 30 CYS HA H 4.44 . 1 174 30 CYS HB2 H 3.09 . 2 175 30 CYS HB3 H 2.92 . 2 176 31 GLY H H 7.43 . 1 177 31 GLY HA2 H 4.23 . 2 178 31 GLY HA3 H 3.35 . 2 179 32 LEU H H 7.10 . 1 180 32 LEU HA H 4.51 . 1 181 32 LEU HB2 H 1.49 . 2 182 32 LEU HB3 H 1.35 . 2 183 32 LEU HG H 1.55 . 1 184 32 LEU HD1 H 0.83 . 2 185 32 LEU HD2 H 0.80 . 2 186 33 PRO HA H 4.13 . 1 187 33 PRO HB2 H 2.22 . 2 188 33 PRO HB3 H 1.79 . 2 189 33 PRO HG2 H 1.99 . 2 190 33 PRO HG3 H 1.92 . 2 191 33 PRO HD2 H 3.75 . 2 192 33 PRO HD3 H 3.54 . 2 193 34 GLY H H 8.31 . 1 194 34 GLY HA2 H 3.85 . 2 195 34 GLY HA3 H 3.81 . 2 196 35 THR H H 7.67 . 1 197 35 THR HA H 4.20 . 1 198 35 THR HB H 3.70 . 1 199 35 THR HG2 H 0.92 . 1 200 36 LYS H H 8.37 . 1 201 36 LYS HA H 4.37 . 1 202 36 LYS HB2 H 1.58 . 1 203 36 LYS HB3 H 1.58 . 1 204 36 LYS HG2 H 1.11 . 1 205 36 LYS HG3 H 1.11 . 1 206 36 LYS HD2 H 1.35 . 2 207 36 LYS HD3 H 1.22 . 2 208 36 LYS HE2 H 2.86 . 2 209 36 LYS HE3 H 2.77 . 2 210 37 CYS H H 7.90 . 1 211 37 CYS HA H 5.08 . 1 212 37 CYS HB2 H 2.35 . 2 213 37 CYS HB3 H 1.99 . 2 214 38 CYS H H 9.65 . 1 215 38 CYS HA H 5.31 . 1 216 38 CYS HB2 H 2.68 . 2 217 38 CYS HB3 H 2.59 . 2 218 39 LYS H H 9.82 . 1 219 39 LYS HA H 4.46 . 1 220 39 LYS HB2 H 1.79 . 1 221 39 LYS HB3 H 1.79 . 1 222 39 LYS HG2 H 1.26 . 1 223 39 LYS HG3 H 1.26 . 1 224 39 LYS HD2 H 1.48 . 1 225 39 LYS HD3 H 1.48 . 1 226 39 LYS HE2 H 2.94 . 1 227 39 LYS HE3 H 2.94 . 1 228 39 LYS HZ H 7.43 . 5 229 40 LYS H H 8.51 . 1 230 40 LYS HA H 3.58 . 1 231 40 LYS HB2 H 1.39 . 2 232 40 LYS HB3 H 1.15 . 2 233 40 LYS HG2 H 1.01 . 1 234 40 LYS HG3 H 1.01 . 1 235 40 LYS HD2 H 1.40 . 1 236 40 LYS HD3 H 1.40 . 1 237 40 LYS HE2 H 2.75 . 1 238 40 LYS HE3 H 2.75 . 1 239 41 PRO HA H 4.05 . 1 240 41 PRO HB2 H 2.02 . 1 241 41 PRO HB3 H 2.02 . 1 242 41 PRO HG2 H 1.72 . 2 243 41 PRO HG3 H 1.57 . 2 244 41 PRO HD2 H 3.09 . 2 245 41 PRO HD3 H 2.90 . 2 stop_ save_