data_4615 #Corrected using PDB structure: 1DKCA # #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 # 26 Q HA 4.19 5.30 # #After reference correction, the following residues still #have a HN chemical shift difference (obs*-pred) greater than 2.0ppm: #NUM AA CS Observed* Predicted # 25 F H 8.45 10.60 # #The average CS difference between predicted and observed: #HA CA CB CO N HN #0.04 N/A N/A N/A N/A -0.18 # #bmr4615.str.corr chemical shifts have been re-referenced with the following #offsets (these values have been added to the original bmr4615.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 +/-0.19 # #The Correlation Coefficients between predicted and observed #chemical shifts are: #HA CA CB CO N HN #0.718 N/A N/A N/A N/A 0.192 # #The RMSD between predicted and observed* (reference #corrected) chemical shifts are: #HA CA CB CO N HN #0.157 N/A N/A N/A N/A 0.565 # ####################### # 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 ; 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_ _BMRB_accession_number 4615 _BMRB_flat_file_name bmr4615.str _Entry_type new _Submission_date 2000-05-05 _Accession_date 2000-09-07 _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' 181 stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _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 _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 _Page_first 10973 _Page_last 10978 _Year 2001 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_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 1DKC ? . stop_ save_ ######################## # Monomeric polymers # ######################## save_antifungal_peptide _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common "antifungal peptide" _Name_variant . _Abbreviation_common . _Mol_thiol_state 'all disulfide bound' ############################## # 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 2004-07-29 _Sequence_homology_query_revised_last_date 2004-04-29 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 "A Chain A, Solution Structure Of Pafp-S, AnAntifungal Peptide From The Seeds Of PhytolaccaAmericana" 100.00 38 100 100 8e-18 DBJ BAA88893.1 "anti-fungal protein precursor[Phytolacca americana]" 58.46 65 100 100 8e-18 GenBank AAC05129.1 "anti-fungal protein precursor[Phytolacca americana]" 58.46 65 100 100 8e-18 GenBank AAD17942.1 "anti-fungal protein [Phytolaccaamericana]" 58.46 65 100 100 8e-18 SWISS-PROT P81418 "PAFP_PHYAM Antimicrobial peptide 1 precursor(AMP1) (Pa-AMP-1) (Anti-fungal protein 1) (AFPS-1)(PAFP-S)" 58.46 65 100 100 8e-18 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 "antifungal peptide" 3 CYS SG "antifungal peptide" 20 CYS SG single disulfide "antifungal peptide" 10 CYS SG "antifungal peptide" 24 CYS SG single disulfide "antifungal peptide" 19 CYS SG "antifungal peptide" 35 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 _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 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_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DMX _Field_strength 600 save_ ############################# # NMR applied experiments # ############################# save_NMR_applied_experiment _Saveframe_category NMR_applied_experiment _Experiment_name ; 2D NOESY DQF-COSY 2D COSY 2D TOCSY E-COSY ; save_ ####################### # Sample conditions # ####################### save_sample_cond_1 _Saveframe_category sample_conditions loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3.5 0.1 n/a temperature 300 1 K 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 0.00 internal direct . internal . . 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 "antifungal peptide" 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 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_