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_