data_4461
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
1H NMR Solution Structure of Cycloviolacin O1 - A Macro-cyclic Polypeptide
Isolated from Viola odorat
;
_BMRB_accession_number 4461
_BMRB_flat_file_name bmr4461.str
_Entry_type original
_Submission_date 1999-11-17
_Accession_date 1999-11-17
_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 Craik David J. .
2 Daly Norelle L. .
3 Bond Trudy . .
4 Waine Clement . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 126
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2000-03-23 original BMRB .
stop_
_Original_release_date 1999-11-21
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full .
_Citation_title
;
Plant Cyclotides - a unique family of cyclic and knotted proteins that defines
the cyclic cystine knot structural moti
;
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code 20069951
_PubMed_ID 10600388
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Craik David J. .
2 Daly Norelle L. .
3 Bond Trudy . .
4 Waine Clement . .
stop_
_Journal_abbreviation 'J. Mol. Biol.'
_Journal_volume 294
_Journal_issue .
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 1327
_Page_last 1336
_Year 1999
_Details .
save_
##################################
# Molecular system description #
##################################
save_cck_system
_Saveframe_category molecular_system
_Mol_system_name 'Cycloviolacin O1'
_Abbreviation_common cck
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
cck $cck
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_cck
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common cyclotide
_Abbreviation_common cck
_Molecular_mass 3116
_Mol_thiol_state 'all disulfide bound'
_Details 'three disulfide bonds that form a knotted core and the backbone is cyclic via a covalent peptide bond'
##############################
# Polymer residue sequence #
##############################
_Residue_count 30
_Mol_residue_sequence
;
SCVYIPCTVTALLGCSCSNR
VCYNGIPCAE
;
loop_
_Residue_seq_code
_Residue_author_seq_code
_Residue_label
1 4 SER 2 5 CYS 3 6 VAL 4 7 TYR 5 8 ILE
6 9 PRO 7 10 CYS 8 11 THR 9 12 VAL 10 13 THR
11 14 ALA 12 15 LEU 13 16 LEU 14 17 GLY 15 18 CYS
16 19 SER 17 20 CYS 18 21 SER 19 22 ASN 20 23 ARG
21 24 VAL 22 25 CYS 23 26 TYR 24 27 ASN 25 28 GLY
26 29 ILE 27 30 PRO 28 1 CYS 29 2 ALA 30 3 GLU
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 1DF6 '1h Nmr Solution Structure Of Cycloviolacin O1' 96.67 30 100.00 100.00 1.16e-07
PDB 1NBJ 'High-Resolution Solution Structure Of Cycloviolacin O1' 90.00 30 100.00 100.00 1.62e-06
SWISS-PROT P82230 Cycloviolacin-O1 80.00 30 100.00 100.00 1.89e-04
stop_
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
$cck Viola 97441 Eukaryota . Violaceae odorata
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
$cck 'purified from the natural source' . . . . .
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_ss1559
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$cck 1.6 mM .
stop_
save_
############################
# Computer software used #
############################
save_PROCHECK-NMR
_Saveframe_category software
_Name ProcheckNMR
_Version .
loop_
_Task
'Ramachandran plot'
stop_
_Details .
save_
save_X-PLOR
_Saveframe_category software
_Name X-PLOR
_Version .
loop_
_Task
'Structure Calculations and energy minimizations'
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_NMR_spectrometer_one
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model AMX
_Field_strength 500
_Details .
save_
save_NMR_spectrometer_two
_Saveframe_category NMR_spectrometer
_Manufacturer Bruker
_Model DMX
_Field_strength 750
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_2D_1H-1H_TOCSY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H TOCSY'
_Sample_label .
save_
save_2D_1H-1H_NOESY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H NOESY'
_Sample_label .
save_
save_2D_1H-1H_E-COSY_3
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H E-COSY'
_Sample_label .
save_
save_2D_1H-1H_DQF-COSY_4
_Saveframe_category NMR_applied_experiment
_Experiment_name '2D 1H-1H DQF-COSY'
_Sample_label .
save_
#######################
# Sample conditions #
#######################
save_ss1559-cond_1
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
pH 3.6 0.3 na
temperature 298 2 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
_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 #
# #
# 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_chem_shift1
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Experiment_label
'2D 1H-1H TOCSY'
stop_
loop_
_Sample_label
$ss1559
stop_
_Sample_conditions_label $ss1559-cond_1
_Chem_shift_reference_set_label $chemical_shift_reference
_Mol_system_component_name cck
_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 SER H H 8.91 0.01 1
2 . 1 SER HA H 4.69 0.01 1
3 . 1 SER HB2 H 3.88 0.01 2
4 . 1 SER HB3 H 4.01 0.01 2
5 . 2 CYS H H 8.24 0.01 1
6 . 2 CYS HA H 5.35 0.01 1
7 . 2 CYS HB2 H 3.13 0.01 2
8 . 2 CYS HB3 H 3.27 0.01 2
9 . 3 VAL H H 7.94 0.01 1
10 . 3 VAL HA H 3.43 0.01 1
11 . 3 VAL HB H 1.44 0.01 1
12 . 3 VAL HG1 H 0.30 0.01 2
13 . 3 VAL HG2 H 0.93 0.01 2
14 . 4 TYR H H 8.20 0.01 1
15 . 4 TYR HA H 4.61 0.01 1
16 . 4 TYR HB2 H 2.89 0.01 2
17 . 4 TYR HB3 H 3.19 0.01 2
18 . 5 ILE H H 7.58 0.01 1
19 . 5 ILE HA H 4.67 0.01 1
20 . 5 ILE HB H 1.90 0.01 1
21 . 5 ILE HG12 H 1.50 0.01 2
22 . 5 ILE HG13 H 1.01 0.01 2
23 . 6 PRO HA H 4.44 0.01 1
24 . 6 PRO HB2 H 2.31 0.01 2
25 . 6 PRO HG2 H 1.87 0.01 2
26 . 6 PRO HD2 H 3.51 0.01 2
27 . 6 PRO HD3 H 3.69 0.01 2
28 . 7 CYS H H 8.33 0.01 1
29 . 7 CYS HA H 4.05 0.01 1
30 . 7 CYS HB2 H 2.70 0.01 2
31 . 7 CYS HB3 H 2.87 0.01 2
32 . 8 THR H H 8.73 0.01 1
33 . 8 THR HA H 4.11 0.01 1
34 . 8 THR HG2 H 1.19 0.01 1
35 . 9 VAL H H 8.84 0.01 1
36 . 9 VAL HA H 3.95 0.01 1
37 . 9 VAL HB H 2.00 0.01 1
38 . 9 VAL HG1 H 0.93 0.01 2
39 . 9 VAL HG2 H 1.00 0.01 2
40 . 10 THR H H 8.54 0.01 1
41 . 10 THR HA H 4.27 0.01 1
42 . 10 THR HB H 4.83 0.01 1
43 . 10 THR HG2 H 1.13 0.01 1
44 . 11 ALA H H 7.99 0.01 1
45 . 11 ALA HA H 4.40 0.01 1
46 . 11 ALA HB H 1.41 0.01 1
47 . 12 LEU H H 7.95 0.01 1
48 . 12 LEU HA H 4.18 0.01 1
49 . 12 LEU HB2 H 1.72 0.01 2
50 . 12 LEU HG H 1.59 0.01 1
51 . 12 LEU HD1 H 0.88 0.01 2
52 . 13 LEU H H 7.52 0.01 1
53 . 13 LEU HA H 4.40 0.01 1
54 . 13 LEU HB2 H 1.75 0.01 2
55 . 13 LEU HB3 H 1.86 0.01 2
56 . 13 LEU HG H 1.56 0.01 1
57 . 13 LEU HD1 H 0.83 0.01 2
58 . 13 LEU HD2 H 0.91 0.01 2
59 . 14 GLY H H 8.19 0.01 1
60 . 14 GLY HA2 H 3.76 0.01 2
61 . 14 GLY HA3 H 4.13 0.01 2
62 . 15 CYS H H 7.69 0.01 1
63 . 15 CYS HA H 4.69 0.01 1
64 . 15 CYS HB2 H 2.49 0.01 2
65 . 15 CYS HB3 H 3.52 0.01 2
66 . 16 SER H H 9.09 0.01 1
67 . 16 SER HA H 4.63 0.01 1
68 . 16 SER HB2 H 3.80 0.01 2
69 . 17 CYS H H 8.77 0.01 1
70 . 17 CYS HA H 4.54 0.01 1
71 . 17 CYS HB2 H 3.00 0.01 2
72 . 18 SER H H 9.47 0.01 1
73 . 18 SER HA H 4.57 0.01 1
74 . 18 SER HB2 H 3.60 0.01 2
75 . 19 ASN H H 9.38 0.01 1
76 . 19 ASN HA H 4.20 0.01 1
77 . 19 ASN HB2 H 2.61 0.01 2
78 . 19 ASN HB3 H 2.93 0.01 2
79 . 20 ARG H H 8.25 0.01 1
80 . 20 ARG HA H 3.44 0.01 1
81 . 20 ARG HB2 H 2.27 0.01 2
82 . 20 ARG HB3 H 1.89 0.01 2
83 . 20 ARG HG2 H 1.49 0.01 2
84 . 21 VAL H H 8.12 0.01 1
85 . 21 VAL HA H 4.35 0.01 1
86 . 21 VAL HB H 2.09 0.01 1
87 . 21 VAL HG1 H 0.91 0.01 2
88 . 21 VAL HG2 H 0.99 0.01 2
89 . 22 CYS H H 8.21 0.01 1
90 . 22 CYS HA H 4.74 0.01 1
91 . 22 CYS HB2 H 2.69 0.01 2
92 . 22 CYS HB3 H 2.97 0.01 2
93 . 23 TYR H H 9.86 0.01 1
94 . 23 TYR HA H 5.02 0.01 1
95 . 23 TYR HB2 H 2.91 0.01 2
96 . 23 TYR HB3 H 2.99 0.01 2
97 . 24 ASN H H 8.66 0.01 1
98 . 24 ASN HA H 4.78 0.01 1
99 . 24 ASN HB2 H 2.71 0.01 2
100 . 24 ASN HB3 H 2.93 0.01 2
101 . 25 GLY H H 7.77 0.01 1
102 . 25 GLY HA2 H 3.33 0.01 2
103 . 25 GLY HA3 H 4.46 0.01 2
104 . 26 ILE H H 7.74 0.01 1
105 . 26 ILE HA H 4.53 0.01 1
106 . 26 ILE HB H 1.94 0.01 1
107 . 26 ILE HG12 H 0.97 0.01 2
108 . 27 PRO HA H 4.19 0.01 1
109 . 27 PRO HB2 H 2.16 0.01 2
110 . 27 PRO HB3 H 2.23 0.01 2
111 . 27 PRO HG2 H 1.78 0.01 2
112 . 27 PRO HG3 H 1.94 0.01 2
113 . 27 PRO HD2 H 3.64 0.01 2
114 . 27 PRO HD3 H 3.84 0.01 2
115 . 28 CYS H H 9.08 0.01 1
116 . 28 CYS HB2 H 3.06 0.01 2
117 . 28 CYS HB3 H 3.17 0.01 2
118 . 29 ALA H H 8.51 0.01 1
119 . 29 ALA HA H 4.14 0.01 1
120 . 29 ALA HB H 1.29 0.01 1
121 . 30 GLU H H 7.91 0.01 1
122 . 30 GLU HA H 4.38 0.01 1
123 . 30 GLU HB2 H 1.61 0.01 2
124 . 30 GLU HB3 H 1.91 0.01 2
125 . 30 GLU HG2 H 2.55 0.01 2
126 . 30 GLU HG3 H 2.76 0.01 2
stop_
save_