data_11172
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
13C and 15N chemical shifts of the membrane-reconstituted subunit c-ring of
E. coli H+-ATP synthase
;
_BMRB_accession_number 11172
_BMRB_flat_file_name bmr11172.str
_Entry_type original
_Submission_date 2010-05-14
_Accession_date 2010-05-14
_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 Todokoro Yasuto . .
2 Kobayashi Masatoshi . .
3 Sato Takeshi . .
4 Kawakami Toru . .
5 Yumen Ikuko . .
6 Aimoto Saburo . .
7 Fujiwara Toshimichi . .
8 Akutsu Hideo . .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 1
stop_
loop_
_Data_type
_Data_type_count
"13C chemical shifts" 127
"15N chemical shifts" 35
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2017-08-03 original BMRB .
stop_
_Original_release_date 2010-05-14
save_
#############################
# Citation for this entry #
#############################
save_citation_1
_Saveframe_category entry_citation
_Citation_full .
_Citation_title
;
Structural analysis of the membrane-reconstituted subunit c-ring of E. coli
H+-ATP synthase by solid-state NMR
;
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code .
_PubMed_ID 20596883
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Todokoro Yasuto . .
2 Kobayashi Masatoshi . .
3 Sato Takeshi . .
4 Kawakami Toru . .
5 Yumen Ikuko . .
6 Aimoto Saburo . .
7 Fujiwara Toshimichi . .
8 Akutsu Hideo . .
stop_
_Journal_abbreviation 'J. Biomol. NMR'
_Journal_name_full 'Journal of Biomolecular NMR'
_Journal_volume 48
_Journal_issue 1
_Journal_ISSN 0925-2738
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 1
_Page_last 11
_Year 2010
_Details .
save_
##################################
# Molecular system description #
##################################
save_assembly
_Saveframe_category molecular_system
_Mol_system_name 'subunit c-ring of FoF1 ATP synthase (EFoc-ring)'
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'FoF1 ATP synthase subunit c (EFoc)' $entity_1
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state ?
_System_paramagnetic no
_System_thiol_state .
_Database_query_date .
_Details 'From E. coli. The EFoc oligomer takes on a ring structure.'
save_
########################
# Monomeric polymers #
########################
save_entity_1
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class protein
_Name_common 'FoF1 ATP synthase subunit c (EFoc)'
_Molecular_mass .
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 79
_Mol_residue_sequence
;
MENLNMDLLYMAAAVMMGLA
AIGAAIGIGILGGKFLEGAA
RQPDLIPLLRTQFFIVMGLV
DAIPMIAVGLGLYVMFAVA
;
loop_
_Residue_seq_code
_Residue_label
1 MET 2 GLU 3 ASN 4 LEU 5 ASN
6 MET 7 ASP 8 LEU 9 LEU 10 TYR
11 MET 12 ALA 13 ALA 14 ALA 15 VAL
16 MET 17 MET 18 GLY 19 LEU 20 ALA
21 ALA 22 ILE 23 GLY 24 ALA 25 ALA
26 ILE 27 GLY 28 ILE 29 GLY 30 ILE
31 LEU 32 GLY 33 GLY 34 LYS 35 PHE
36 LEU 37 GLU 38 GLY 39 ALA 40 ALA
41 ARG 42 GLN 43 PRO 44 ASP 45 LEU
46 ILE 47 PRO 48 LEU 49 LEU 50 ARG
51 THR 52 GLN 53 PHE 54 PHE 55 ILE
56 VAL 57 MET 58 GLY 59 LEU 60 VAL
61 ASP 62 ALA 63 ILE 64 PRO 65 MET
66 ILE 67 ALA 68 VAL 69 GLY 70 LEU
71 GLY 72 LEU 73 TYR 74 VAL 75 MET
76 PHE 77 ALA 78 VAL 79 ALA
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
_Strain
$entity_1 'E. coli' 562 Eubacteria . Escherichia coli MEG119
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
$entity_1 'recombinant technology' . Escherichia coli . pCP35
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_sample_1
_Saveframe_category sample
_Sample_type membrane
_Details
;
The EFoc is in DMPC-d54 bilayers. Protein/lipid molar ratio is 1:40.
The sample is hydrated. De-ionized water/total ratio is 10-50%.
;
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Concentration_min_value
_Concentration_max_value
_Isotopic_labeling
$entity_1 6 mg . . '[U-13C; U-15N]'
DMPC-d54 21.3 mg . . '2H-hydrocarbon chain'
H2O . % 10 50 'natural abundance'
NaN3 1 mM . . 'natural abundance'
Tris-HCl 10 mM . . 'natural abundance'
stop_
save_
save_sample_2
_Saveframe_category sample
_Sample_type membrane
_Details 'The EFoc is in DMPC-d54 bilayers. Protein/lipid molar ratio is 1:40.'
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$entity_1 6 mg '[3-13C]-Ala24, [4-13C]-Asp61'
H2O 100 % 'natural abundance'
DMPC-d54 21.3 mg '2H-hydrocarbon chain'
NaN3 1 mM 'natural abundance'
Tris-HCl 10 mM 'natural abundance'
stop_
save_
############################
# Computer software used #
############################
save_FELIX
_Saveframe_category software
_Name FELIX
_Version 2007
loop_
_Vendor
_Address
_Electronic_address
'Felix NMR Inc., San Diego, CA' . .
stop_
loop_
_Task
processing
stop_
_Details .
save_
save_SPARKY
_Saveframe_category software
_Name SPARKY
_Version .
loop_
_Vendor
_Address
_Electronic_address
Goddard . .
stop_
loop_
_Task
'chemical shift assignment'
stop_
_Details .
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer Varian
_Model Infinity-plus
_Field_strength 600
_Details .
save_
save_spectrometer_2
_Saveframe_category NMR_spectrometer
_Manufacturer Varian
_Model Infinity-plus
_Field_strength 500
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_Intra-residue_2D_13C-13C_DARR_1
_Saveframe_category NMR_applied_experiment
_Experiment_name 'Intra-residue 2D 13C-13C DARR'
_Sample_label $sample_1
save_
save_Inter-residue_2D_CACA_2
_Saveframe_category NMR_applied_experiment
_Experiment_name 'Inter-residue 2D CACA'
_Sample_label $sample_1
save_
save_Intra-residue_2D_NCACB_3
_Saveframe_category NMR_applied_experiment
_Experiment_name 'Intra-residue 2D NCACB'
_Sample_label $sample_1
save_
save_Inter-residue_2D_N(CO)CACB_4
_Saveframe_category NMR_applied_experiment
_Experiment_name 'Inter-residue 2D N(CO)CACB'
_Sample_label $sample_1
save_
save_Inter-residue_3D_N(CO)CA_5
_Saveframe_category NMR_applied_experiment
_Experiment_name 'Inter-residue 3D N(CO)CA'
_Sample_label $sample_1
save_
save_Intra-residue_3D_NCACO_6
_Saveframe_category NMR_applied_experiment
_Experiment_name 'Intra-residue 3D NCACO'
_Sample_label $sample_1
save_
save_2H-selective_1H-depolarization_13C-NMR(CODSHD)_7
_Saveframe_category NMR_applied_experiment
_Experiment_name '2H-selective 1H-depolarization 13C-NMR(CODSHD)'
_Sample_label $sample_1
save_
save_13C_rotational_resonance_8
_Saveframe_category NMR_applied_experiment
_Experiment_name '13C rotational resonance'
_Sample_label $sample_2
save_
#######################
# Sample conditions #
#######################
save_condition_233K
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
pH 8.0 . pH
temperature 233 . K
stop_
save_
save_condition_223K
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
pH 8.0 . pH
temperature 223 . K
stop_
save_
save_condition_193K
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
pH 8.0 . pH
temperature 193 . K
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_reference_1
_Saveframe_category chemical_shift_reference
_Details
;
The 13C chemical shift was referenced to DSS by using the methine carbon signal
of adamantane under MAS at 40.5 ppm relative to DSS.
The 15N chemical shift was referenced to that of liquid NH3 deduced from the 13C
chemical shift using the 15N/13C ratio following the IUPAC recommendation.
;
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
adamantane C 13 'methine carbon' ppm 40.5 external direct . . . 1.0
DSS N 15 'methyl carbon' ppm 0.00 na indirect . . . 0.402979946
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_1
_Saveframe_category assigned_chemical_shifts
_Details 'In the ring structure, the side chain of essential Asp61 takes on the COOH state.'
loop_
_Software_label
$SPARKY
stop_
loop_
_Experiment_label
'Intra-residue 2D 13C-13C DARR'
'Inter-residue 2D CACA'
'Intra-residue 2D NCACB'
'Inter-residue 2D N(CO)CACB'
'Inter-residue 3D N(CO)CA'
'Intra-residue 3D NCACO'
'2H-selective 1H-depolarization 13C-NMR(CODSHD)'
'13C rotational resonance'
stop_
loop_
_Sample_label
$sample_1
$sample_2
stop_
_Sample_conditions_label $condition_233K
_Chem_shift_reference_set_label $reference_1
_Mol_system_component_name 'FoF1 ATP synthase subunit c (EFoc)'
_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 21 21 ALA C C 179 1 1
2 21 21 ALA CA C 55.4 1 1
3 21 21 ALA CB C 18.3 2 1
4 21 21 ALA N N 120 3 1
5 22 22 ILE C C 178 1 1
6 22 22 ILE CA C 66.2 0.9 1
7 22 22 ILE CB C 38.0 1 1
8 22 22 ILE CD1 C 14.7 1.3 1
9 22 22 ILE CG1 C 29.2 1.5 1
10 22 22 ILE CG2 C 17.2 1.4 1
11 22 22 ILE N N 118 2 1
12 23 23 GLY C C 175 1 1
13 23 23 GLY CA C 48.4 0.6 1
14 23 23 GLY N N 107 2 1
15 24 24 ALA C C 179 2 1
16 24 24 ALA CA C 55.3 0.7 1
17 24 24 ALA CB C 18.4 1 1
18 24 24 ALA N N 121 3 1
19 25 25 ALA C C 179 2 1
20 25 25 ALA CA C 55.7 1 1
21 25 25 ALA CB C 18.3 2 1
22 25 25 ALA N N 120 3 1
23 26 26 ILE C C 178 1 1
24 26 26 ILE CA C 66.6 0.9 1
25 26 26 ILE CB C 38.0 1 1
26 26 26 ILE CD1 C 14.7 1.3 1
27 26 26 ILE CG1 C 29.2 1.5 1
28 26 26 ILE CG2 C 17.2 1.4 1
29 26 26 ILE N N 118 5 1
30 27 27 GLY C C 175 1 1
31 27 27 GLY CA C 47.7 0.7 1
32 27 27 GLY N N 107 2 1
33 28 28 ILE C C 178 1 1
34 28 28 ILE CA C 65.9 0.7 1
35 28 28 ILE CB C 38.0 1 1
36 28 28 ILE CD1 C 14.7 1.3 1
37 28 28 ILE CG1 C 29.2 1.5 1
38 28 28 ILE CG2 C 17.2 1.4 1
39 28 28 ILE N N 119 2 1
40 29 29 GLY C C 175 1 1
41 29 29 GLY CA C 47.6 0.7 1
42 29 29 GLY N N 106 2 1
43 30 30 ILE C C 178 1 1
44 30 30 ILE CA C 65.9 0.7 1
45 30 30 ILE CB C 38.0 1 1
46 30 30 ILE CD1 C 14.7 1.3 1
47 30 30 ILE CG1 C 29.2 1.5 1
48 30 30 ILE CG2 C 17.2 1.4 1
49 30 30 ILE N N 120 2 1
50 31 31 LEU C C 179 1 1
51 31 31 LEU CA C 58.5 0.7 1
52 31 31 LEU CB C 41.4 1.4 1
53 31 31 LEU CD1 C 23.4 1.9 2
54 31 31 LEU CD2 C 23.4 1.9 2
55 31 31 LEU CG C 26.8 1.4 1
56 31 31 LEU N N 119 1 1
57 32 32 GLY C C 175 1 1
58 32 32 GLY CA C 47.5 0.7 1
59 32 32 GLY N N 108 2 1
60 33 33 GLY C C 175 1 1
61 33 33 GLY CA C 47.5 0.7 1
62 33 33 GLY N N 108 1 1
63 34 34 LYS C C 179 1 1
64 34 34 LYS CA C 58.0 0.8 1
65 34 34 LYS N N 120 2 1
66 37 37 GLU C C 179 1 1
67 37 37 GLU CA C 59.8 0.7 1
68 37 37 GLU N N 120 2 1
69 38 38 GLY C C 175 1 1
70 38 38 GLY CA C 47.0 0.8 1
71 38 38 GLY N N 108 1 1
72 39 39 ALA C C 179 1 1
73 39 39 ALA CA C 53.6 0.7 1
74 39 39 ALA CB C 18.9 1.5 1
75 39 39 ALA N N 122 3 1
76 42 42 GLN C C 174 1 1
77 42 42 GLN CA C 55.3 0.7 1
78 42 42 GLN N N 120 3 1
79 43 43 PRO CA C 62.0 1 1
80 43 43 PRO N N 134 1 1
81 51 51 THR C C 178 1 1
82 51 51 THR CA C 65.5 1 1
83 51 51 THR CB C 67.3 1 1
84 51 51 THR N N 116 3 1
85 55 55 ILE C C 178 1 1
86 55 55 ILE CA C 65.9 0.6 1
87 55 55 ILE CB C 38.0 1 1
88 55 55 ILE CD1 C 14.7 1.3 1
89 55 55 ILE CG1 C 29.2 1.5 1
90 55 55 ILE CG2 C 17.2 1.4 1
91 55 55 ILE N N 119 3 1
92 56 56 VAL CA C 66.2 0.6 1
93 56 56 VAL CB C 31.3 1 1
94 56 56 VAL CG1 C 22.7 1.7 2
95 56 56 VAL CG2 C 22.7 1.7 2
96 57 57 MET C C 179 1 1
97 57 57 MET CA C 58.7 0.7 1
98 57 57 MET N N 119 3 1
99 58 58 GLY C C 175 1 1
100 58 58 GLY CA C 47.8 0.8 1
101 58 58 GLY N N 107 2 1
102 59 59 LEU C C 179 2 1
103 59 59 LEU CA C 58.2 0.8 1
104 59 59 LEU CB C 41.4 1.4 1
105 59 59 LEU CD1 C 23.4 1.9 2
106 59 59 LEU CD2 C 23.4 1.9 2
107 59 59 LEU CG C 26.8 1.4 1
108 59 59 LEU N N 122 2 1
109 61 61 ASP CG C 179.6 1.2 1
110 67 67 ALA C C 179 2 1
111 67 67 ALA CA C 55.6 0.7 1
112 67 67 ALA CB C 18.3 2 1
113 67 67 ALA N N 119 2 1
114 68 68 VAL C C 178 1 1
115 68 68 VAL CA C 66.4 0.9 1
116 68 68 VAL CB C 31.3 1 1
117 68 68 VAL CG1 C 22.7 1.7 2
118 68 68 VAL CG2 C 22.7 1.7 2
119 68 68 VAL N N 119 3 1
120 69 69 GLY C C 175 1 1
121 69 69 GLY CA C 47.9 0.8 1
122 69 69 GLY N N 108 2 1
123 70 70 LEU C C 179 1 1
124 70 70 LEU CA C 58.2 0.8 1
125 70 70 LEU CB C 41.4 1.4 1
126 70 70 LEU CD1 C 23.4 1.9 2
127 70 70 LEU CD2 C 23.4 1.9 2
128 70 70 LEU CG C 26.8 1.4 1
129 70 70 LEU N N 122 2 1
130 71 71 GLY C C 175 1 1
131 71 71 GLY CA C 47.9 0.8 1
132 71 71 GLY N N 108 2 1
133 72 72 LEU C C 178 1 1
134 72 72 LEU CA C 58.2 0.8 1
135 72 72 LEU CB C 41.4 1.4 1
136 72 72 LEU CD1 C 23.4 1.9 2
137 72 72 LEU CD2 C 23.4 1.9 2
138 72 72 LEU CG C 26.8 1.4 1
139 72 72 LEU N N 122 2 1
140 73 73 TYR C C 178 1 1
141 73 73 TYR CA C 60.4 0.6 1
142 73 73 TYR CB C 41.1 0.6 1
143 73 73 TYR N N 119 3 1
144 74 74 VAL C C 178 1 1
145 74 74 VAL CA C 66.9 0.6 1
146 74 74 VAL CB C 31.3 1 1
147 74 74 VAL CG1 C 22.7 1.7 2
148 74 74 VAL CG2 C 22.7 1.7 2
149 74 74 VAL N N 118 3 1
150 76 76 PHE C C 174 1 1
151 76 76 PHE CA C 59.5 0.7 1
152 76 76 PHE N N 116 1 1
153 77 77 ALA C C 175 1 1
154 77 77 ALA CA C 50.7 0.7 1
155 77 77 ALA CB C 20.0 0.6 1
156 77 77 ALA N N 127 2 1
157 78 78 VAL C C 177 1 1
158 78 78 VAL CA C 61.7 0.7 1
159 78 78 VAL CB C 35.5 1.4 1
160 78 78 VAL CG1 C 21.4 1.4 2
161 78 78 VAL CG2 C 21.4 1.4 2
162 78 78 VAL N N 118 1 1
stop_
save_