data_4615 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Solution Structure of PAFP-S: A new Knottin-type Antifungal Peptide from the seeds of Phytolacca americana ; _BMRB_accession_number 4615 _BMRB_flat_file_name bmr4615.str _Entry_type original _Submission_date 2000-05-05 _Accession_date 2000-09-07 _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 Gao G. H. . 2 Liu W. . . 3 Dai J. X. . 4 Wang J. F. . 5 Hu Z. . . 6 Zhang Y. . . 7 Wang D. C. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 181 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2002-01-23 original BMRB . stop_ _Original_release_date 2000-09-07 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Solution Structure of PAFP-S: A new Knottin-type Antifungal Peptide from the seeds of Phytolacca americana ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 21435646 _PubMed_ID 11551192 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Gao G. H. . 2 Liu W. . . 3 Dai J. X. . 4 Wang J. F. . 5 Hu Z. . . 6 Zhang Y. . . 7 Wang D. C. . stop_ _Journal_abbreviation Biochemistry _Journal_volume 40 _Journal_issue 37 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 10973 _Page_last 10978 _Year 2001 _Details . loop_ _Keyword 'antifungal peptide' 'knottin-like motif' 'solution structure' stop_ save_ ################################## # Molecular system description # ################################## save_system_antifungal_peptide _Saveframe_category molecular_system _Mol_system_name 'antifungal peptide' _Abbreviation_common 'antifungal peptide' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'antifungal peptide' $antifungal_peptide stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'all disulfide bound' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_antifungal_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'antifungal peptide' _Molecular_mass . _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 38 _Mol_residue_sequence ; AGCIKNGGRCNASAGPPYCC SSYCFQIAGQSYGVCKNR ; loop_ _Residue_seq_code _Residue_label 1 ALA 2 GLY 3 CYS 4 ILE 5 LYS 6 ASN 7 GLY 8 GLY 9 ARG 10 CYS 11 ASN 12 ALA 13 SER 14 ALA 15 GLY 16 PRO 17 PRO 18 TYR 19 CYS 20 CYS 21 SER 22 SER 23 TYR 24 CYS 25 PHE 26 GLN 27 ILE 28 ALA 29 GLY 30 GLN 31 SER 32 TYR 33 GLY 34 VAL 35 CYS 36 LYS 37 ASN 38 ARG stop_ _Sequence_homology_query_date 2008-08-19 _Sequence_homology_query_revised_last_date 2008-08-19 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 1DKC 'Solution Structure Of Pafp-S, An Antifungal Peptide From The Seeds Of Phytolacca Americana' 97.37 38 100.00 100.00 3.61e-12 DBJ BAA88893 'anti-fungal protein precursor [Phytolacca americana]' 100.00 65 100.00 100.00 4.52e-14 GenBank AAC05129 'anti-fungal protein precursor [Phytolacca americana]' 100.00 65 100.00 100.00 4.52e-14 GenBank AAD17942 'anti-fungal protein [Phytolacca americana]' 100.00 65 100.00 100.00 4.52e-14 SWISS-PROT P81418 'Antimicrobial peptide 1 precursor (Pa-AMP-1) (AMP1) (Anti-fungal protein 1) (AFPS-1) (PAFP-S)' 100.00 65 100.00 100.00 4.52e-14 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Details $antifungal_peptide Pokeweed 3527 Eukaryota Viridiplantae Phytolacca americana seed 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 $antifungal_peptide 'purified from natural source' . . . . . 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 _Isotopic_labeling $antifungal_peptide 4 mM . DSS 0.2 mM . stop_ save_ ############################ # Computer software used # ############################ save_UXNMR _Saveframe_category software _Name UXNMR _Version 1.0 loop_ _Task COLLECTION stop_ _Details BRUKER save_ save_FELIX _Saveframe_category software _Name FELIX _Version 97 loop_ _Task PROCESSING stop_ _Details BIOSYM save_ save_X-PLOR _Saveframe_category software _Name X-PLOR _Version 3.851 loop_ _Task REFINEMENT stop_ _Details BRUNGER save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_NOESY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D NOESY' _Sample_label $sample_1 save_ save_DQF-COSY_2 _Saveframe_category NMR_applied_experiment _Experiment_name DQF-COSY _Sample_label $sample_1 save_ save_2D_COSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D COSY' _Sample_label $sample_1 save_ save_2D_TOCSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D TOCSY' _Sample_label $sample_1 save_ save_E-COSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name E-COSY _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.5 0.1 pH temperature 300 1 K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _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 DSS H 1 'methyl protons' ppm 0.00 internal direct . internal . 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_chemical_shift_set_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D NOESY' DQF-COSY '2D COSY' '2D TOCSY' E-COSY stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_cond_1 _Chem_shift_reference_set_label $chemical_shift_reference _Mol_system_component_name 'antifungal peptide' _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 ALA H H 7.78 . 1 2 . 1 ALA HA H 4.46 . 1 3 . 1 ALA HB H 1.52 . 1 4 . 2 GLY H H 8.11 . 1 5 . 2 GLY HA2 H 4.07 . 2 6 . 3 CYS H H 8.13 . 1 7 . 3 CYS HA H 5.07 . 1 8 . 3 CYS HB2 H 3.28 . 2 9 . 3 CYS HB3 H 3.23 . 2 10 . 4 ILE H H 9.03 . 1 11 . 4 ILE HA H 4.08 . 1 12 . 4 ILE HB H 1.90 . 2 13 . 4 ILE HG12 H 1.40 . 2 14 . 4 ILE HG13 H 1.00 . 2 15 . 4 ILE HG2 H 1.06 . 1 16 . 4 ILE HD1 H 0.80 . 1 17 . 5 LYS H H 8.87 . 1 18 . 5 LYS HA H 4.08 . 1 19 . 5 LYS HB2 H 1.84 . 2 20 . 5 LYS HG2 H 1.56 . 2 21 . 5 LYS HD2 H 1.74 . 2 22 . 5 LYS HE2 H 3.23 . 2 23 . 5 LYS HZ H 7.22 . 1 24 . 6 ASN H H 8.47 . 1 25 . 6 ASN HA H 4.97 . 1 26 . 6 ASN HB2 H 2.94 . 2 27 . 6 ASN HB3 H 2.67 . 2 28 . 6 ASN HD21 H 7.51 . 2 29 . 6 ASN HD22 H 6.93 . 2 30 . 7 GLY H H 9.23 . 1 31 . 7 GLY HA2 H 4.49 . 2 32 . 7 GLY HA3 H 3.56 . 2 33 . 8 GLY H H 8.55 . 1 34 . 8 GLY HA2 H 4.19 . 2 35 . 8 GLY HA3 H 3.49 . 2 36 . 9 ARG H H 8.18 . 1 37 . 9 ARG HA H 4.78 . 1 38 . 9 ARG HB2 H 1.73 . 2 39 . 9 ARG HB3 H 1.63 . 2 40 . 9 ARG HG2 H 1.53 . 2 41 . 9 ARG HD2 H 2.62 . 2 42 . 9 ARG HE H 6.77 . 1 43 . 10 CYS H H 8.22 . 1 44 . 10 CYS HA H 4.96 . 1 45 . 10 CYS HB2 H 3.22 . 1 46 . 10 CYS HB3 H 3.08 . 1 47 . 11 ASN H H 8.83 . 1 48 . 11 ASN HA H 4.91 . 1 49 . 11 ASN HB2 H 2.90 . 2 50 . 11 ASN HB3 H 2.71 . 2 51 . 11 ASN HD21 H 7.48 . 2 52 . 11 ASN HD22 H 6.88 . 2 53 . 12 ALA H H 8.99 . 1 54 . 12 ALA HA H 4.19 . 1 55 . 12 ALA HB H 1.38 . 1 56 . 13 SER H H 8.28 . 1 57 . 13 SER HA H 4.57 . 1 58 . 13 SER HB2 H 3.93 . 2 59 . 14 ALA H H 7.58 . 1 60 . 14 ALA HA H 4.74 . 1 61 . 14 ALA HB H 1.36 . 1 62 . 15 GLY H H 7.89 . 1 63 . 15 GLY HA2 H 3.26 . 2 64 . 16 PRO HA H 4.38 . 1 65 . 16 PRO HB2 H 2.39 . 2 66 . 16 PRO HB3 H 1.99 . 2 67 . 16 PRO HG2 H 2.22 . 2 68 . 16 PRO HD2 H 3.02 . 2 69 . 17 PRO HA H 4.20 . 1 70 . 17 PRO HB2 H 2.25 . 2 71 . 17 PRO HB3 H 1.91 . 2 72 . 17 PRO HG2 H 1.83 . 2 73 . 17 PRO HG3 H 1.68 . 2 74 . 17 PRO HD2 H 3.13 . 2 75 . 18 TYR H H 8.80 . 1 76 . 18 TYR HA H 4.96 . 1 77 . 18 TYR HB2 H 3.41 . 1 78 . 18 TYR HB3 H 2.67 . 1 79 . 18 TYR HD1 H 7.19 . 3 80 . 18 TYR HE1 H 6.85 . 3 81 . 19 CYS H H 9.54 . 1 82 . 19 CYS HA H 5.08 . 1 83 . 19 CYS HB2 H 3.67 . 1 84 . 19 CYS HB3 H 2.35 . 1 85 . 20 CYS H H 10.13 . 1 86 . 20 CYS HA H 4.47 . 1 87 . 20 CYS HB2 H 3.28 . 1 88 . 20 CYS HB3 H 2.95 . 1 89 . 21 SER H H 9.71 . 1 90 . 21 SER HA H 4.35 . 1 91 . 21 SER HB2 H 4.35 . 2 92 . 22 SER H H 7.97 . 1 93 . 22 SER HA H 4.01 . 1 94 . 22 SER HB2 H 4.27 . 2 95 . 22 SER HB3 H 4.15 . 2 96 . 23 TYR H H 8.57 . 1 97 . 23 TYR HA H 5.03 . 1 98 . 23 TYR HB2 H 3.44 . 1 99 . 23 TYR HB3 H 2.59 . 1 100 . 23 TYR HD1 H 7.03 . 3 101 . 23 TYR HE1 H 6.79 . 3 102 . 24 CYS H H 8.48 . 1 103 . 24 CYS HA H 4.71 . 1 104 . 24 CYS HB2 H 3.15 . 1 105 . 24 CYS HB3 H 2.74 . 1 106 . 25 PHE H H 8.63 . 1 107 . 25 PHE HA H 4.23 . 1 108 . 25 PHE HB2 H 3.10 . 1 109 . 25 PHE HB3 H 2.46 . 1 110 . 25 PHE HD1 H 7.36 . 3 111 . 25 PHE HE1 H 7.26 . 3 112 . 25 PHE HZ H 6.78 . 1 113 . 26 GLN H H 8.08 . 1 114 . 26 GLN HA H 4.15 . 1 115 . 26 GLN HB2 H 1.71 . 2 116 . 26 GLN HB3 H 1.60 . 2 117 . 26 GLN HG2 H 2.02 . 2 118 . 26 GLN HG3 H 1.88 . 2 119 . 26 GLN HE21 H 6.94 . 2 120 . 26 GLN HE22 H 6.32 . 2 121 . 27 ILE H H 8.22 . 1 122 . 27 ILE HA H 3.90 . 1 123 . 27 ILE HB H 1.52 . 2 124 . 27 ILE HG12 H 1.30 . 2 125 . 27 ILE HG13 H 1.02 . 2 126 . 27 ILE HG2 H 0.86 . 1 127 . 27 ILE HD1 H 0.86 . 1 128 . 28 ALA H H 8.38 . 1 129 . 28 ALA HA H 4.06 . 1 130 . 28 ALA HB H 1.36 . 1 131 . 29 GLY H H 8.65 . 1 132 . 29 GLY HA2 H 4.23 . 2 133 . 29 GLY HA3 H 3.63 . 2 134 . 30 GLN H H 7.99 . 1 135 . 30 GLN HA H 4.59 . 1 136 . 30 GLN HB2 H 1.99 . 2 137 . 30 GLN HG2 H 2.23 . 2 138 . 30 GLN HE21 H 7.53 . 2 139 . 30 GLN HE22 H 6.69 . 2 140 . 31 SER H H 8.84 . 1 141 . 31 SER HA H 4.23 . 1 142 . 31 SER HB2 H 3.87 . 2 143 . 31 SER HB3 H 3.79 . 2 144 . 32 TYR H H 7.26 . 1 145 . 32 TYR HA H 4.88 . 1 146 . 32 TYR HB2 H 3.14 . 2 147 . 32 TYR HB3 H 3.04 . 2 148 . 32 TYR HD1 H 7.07 . 3 149 . 32 TYR HE1 H 6.76 . 3 150 . 33 GLY H H 9.02 . 1 151 . 33 GLY HA2 H 4.70 . 2 152 . 33 GLY HA3 H 3.66 . 2 153 . 34 VAL H H 8.60 . 1 154 . 34 VAL HA H 5.16 . 1 155 . 34 VAL HB H 1.92 . 2 156 . 34 VAL HG1 H 1.00 . 2 157 . 35 CYS H H 8.77 . 1 158 . 35 CYS HA H 5.26 . 1 159 . 35 CYS HB2 H 3.61 . 1 160 . 35 CYS HB3 H 2.79 . 1 161 . 36 LYS H H 8.67 . 1 162 . 36 LYS HA H 4.60 . 1 163 . 36 LYS HB2 H 1.88 . 1 164 . 36 LYS HB3 H 1.70 . 1 165 . 36 LYS HG2 H 1.43 . 2 166 . 36 LYS HD2 H 1.43 . 2 167 . 36 LYS HE2 H 2.75 . 2 168 . 36 LYS HZ H 7.15 . 1 169 . 37 ASN H H 8.52 . 1 170 . 37 ASN HA H 4.95 . 1 171 . 37 ASN HB2 H 2.87 . 1 172 . 37 ASN HB3 H 2.69 . 1 173 . 37 ASN HD21 H 7.68 . 2 174 . 37 ASN HD22 H 6.98 . 2 175 . 38 ARG H H 8.41 . 1 176 . 38 ARG HA H 3.74 . 1 177 . 38 ARG HB2 H 1.57 . 2 178 . 38 ARG HB3 H 1.43 . 2 179 . 38 ARG HG2 H 1.24 . 2 180 . 38 ARG HD2 H 2.83 . 2 181 . 38 ARG HE H 7.02 . 1 stop_ save_