1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Hagn, F.X.
Etzkorn, M.
Raschle, T.
Wagner, G.
Membrane Protein Structures by Solution NMR (MPSbyNMR)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
135
1919
1925
10.1021/ja310901f
23294159
Optimized phospholipid bilayer nanodiscs facilitate high-resolution structure determination of membrane proteins.
2013
10.2210/pdb2m06/pdb
pdb_00002m06
16395.812
Outer membrane protein X
UNP residues 24-171
1
man
polymer
no
no
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIY
GVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIY
GVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF
A
MPSbyNMR-013
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
K12
sample
ompX, ybiG, b0814, JW0799
83333
Escherichia coli
469008
Escherichia coli
BL21 (DE3)
pET11a
Membrane Protein Structures by Solution NMR
MPSbyNMR
PSI:Biology
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Database references
Database references
Data collection
Database references
Other
1
0
2012-12-12
1
1
2013-01-23
1
2
2013-02-20
1
3
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
chemical shifts in DHPC detergent micelles
NMR structure of OmpX in DHPC micelles
Crystal Structure of OmpX
Y
BMRB
Y
RCSB
2012-10-21
REL
REL
REL
REL
58
0
41
17
0
69
structures with the least restraint violations
50
20
2D 1H-15N HSQC
3D HNCO
3D HNCA
3D HN(CO)CA
3D HN(CA)CO
3D HNCACB
3D 1H-15N NOESY
20
mM
50
mM
10
mM
[U-2H]
0.05
%
0.8
mM
[U-13C; U-15N; U-2H]
100
6.5
ambient
318
K
simulated annealing
1
fewest violations
20 mM potassium phosphate, 50 mM sodium chloride, 10 mM [U-2H] EDTA, 0.05 % sodium azide, 0.8 mM [U-13C; U-15N; U-2H] protein, 95% H2O/5% D2O
95% H2O/5% D2O
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Bruker Biospin
collection
TopSpin
Bruker Biospin
processing
TopSpin
Goddard
chemical shift assignment
Sparky
Goddard
peak picking
Sparky
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR NIH
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
750
Bruker
AVANCE
Bruker Avance
800
Bruker
AVANCE
Bruker Avance
ALA
1
n
1
ALA
1
A
THR
2
n
2
THR
2
A
SER
3
n
3
SER
3
A
THR
4
n
4
THR
4
A
VAL
5
n
5
VAL
5
A
THR
6
n
6
THR
6
A
GLY
7
n
7
GLY
7
A
GLY
8
n
8
GLY
8
A
TYR
9
n
9
TYR
9
A
ALA
10
n
10
ALA
10
A
GLN
11
n
11
GLN
11
A
SER
12
n
12
SER
12
A
ASP
13
n
13
ASP
13
A
ALA
14
n
14
ALA
14
A
GLN
15
n
15
GLN
15
A
GLY
16
n
16
GLY
16
A
GLN
17
n
17
GLN
17
A
MET
18
n
18
MET
18
A
ASN
19
n
19
ASN
19
A
LYS
20
n
20
LYS
20
A
MET
21
n
21
MET
21
A
GLY
22
n
22
GLY
22
A
GLY
23
n
23
GLY
23
A
PHE
24
n
24
PHE
24
A
ASN
25
n
25
ASN
25
A
LEU
26
n
26
LEU
26
A
LYS
27
n
27
LYS
27
A
TYR
28
n
28
TYR
28
A
ARG
29
n
29
ARG
29
A
TYR
30
n
30
TYR
30
A
GLU
31
n
31
GLU
31
A
GLU
32
n
32
GLU
32
A
ASP
33
n
33
ASP
33
A
ASN
34
n
34
ASN
34
A
SER
35
n
35
SER
35
A
PRO
36
n
36
PRO
36
A
LEU
37
n
37
LEU
37
A
GLY
38
n
38
GLY
38
A
VAL
39
n
39
VAL
39
A
ILE
40
n
40
ILE
40
A
GLY
41
n
41
GLY
41
A
SER
42
n
42
SER
42
A
PHE
43
n
43
PHE
43
A
THR
44
n
44
THR
44
A
TYR
45
n
45
TYR
45
A
THR
46
n
46
THR
46
A
GLU
47
n
47
GLU
47
A
LYS
48
n
48
LYS
48
A
SER
49
n
49
SER
49
A
ARG
50
n
50
ARG
50
A
THR
51
n
51
THR
51
A
ALA
52
n
52
ALA
52
A
SER
53
n
53
SER
53
A
SER
54
n
54
SER
54
A
GLY
55
n
55
GLY
55
A
ASP
56
n
56
ASP
56
A
TYR
57
n
57
TYR
57
A
ASN
58
n
58
ASN
58
A
LYS
59
n
59
LYS
59
A
ASN
60
n
60
ASN
60
A
GLN
61
n
61
GLN
61
A
TYR
62
n
62
TYR
62
A
TYR
63
n
63
TYR
63
A
GLY
64
n
64
GLY
64
A
ILE
65
n
65
ILE
65
A
THR
66
n
66
THR
66
A
ALA
67
n
67
ALA
67
A
GLY
68
n
68
GLY
68
A
PRO
69
n
69
PRO
69
A
ALA
70
n
70
ALA
70
A
TYR
71
n
71
TYR
71
A
ARG
72
n
72
ARG
72
A
ILE
73
n
73
ILE
73
A
ASN
74
n
74
ASN
74
A
ASP
75
n
75
ASP
75
A
TRP
76
n
76
TRP
76
A
ALA
77
n
77
ALA
77
A
SER
78
n
78
SER
78
A
ILE
79
n
79
ILE
79
A
TYR
80
n
80
TYR
80
A
GLY
81
n
81
GLY
81
A
VAL
82
n
82
VAL
82
A
VAL
83
n
83
VAL
83
A
GLY
84
n
84
GLY
84
A
VAL
85
n
85
VAL
85
A
GLY
86
n
86
GLY
86
A
TYR
87
n
87
TYR
87
A
GLY
88
n
88
GLY
88
A
LYS
89
n
89
LYS
89
A
PHE
90
n
90
PHE
90
A
GLN
91
n
91
GLN
91
A
THR
92
n
92
THR
92
A
THR
93
n
93
THR
93
A
GLU
94
n
94
GLU
94
A
TYR
95
n
95
TYR
95
A
PRO
96
n
96
PRO
96
A
THR
97
n
97
THR
97
A
TYR
98
n
98
TYR
98
A
LYS
99
n
99
LYS
99
A
HIS
100
n
100
HIS
100
A
ASP
101
n
101
ASP
101
A
THR
102
n
102
THR
102
A
SER
103
n
103
SER
103
A
ASP
104
n
104
ASP
104
A
TYR
105
n
105
TYR
105
A
GLY
106
n
106
GLY
106
A
PHE
107
n
107
PHE
107
A
SER
108
n
108
SER
108
A
TYR
109
n
109
TYR
109
A
GLY
110
n
110
GLY
110
A
ALA
111
n
111
ALA
111
A
GLY
112
n
112
GLY
112
A
LEU
113
n
113
LEU
113
A
GLN
114
n
114
GLN
114
A
PHE
115
n
115
PHE
115
A
ASN
116
n
116
ASN
116
A
PRO
117
n
117
PRO
117
A
MET
118
n
118
MET
118
A
GLU
119
n
119
GLU
119
A
ASN
120
n
120
ASN
120
A
VAL
121
n
121
VAL
121
A
ALA
122
n
122
ALA
122
A
LEU
123
n
123
LEU
123
A
ASP
124
n
124
ASP
124
A
PHE
125
n
125
PHE
125
A
SER
126
n
126
SER
126
A
TYR
127
n
127
TYR
127
A
GLU
128
n
128
GLU
128
A
GLN
129
n
129
GLN
129
A
SER
130
n
130
SER
130
A
ARG
131
n
131
ARG
131
A
ILE
132
n
132
ILE
132
A
ARG
133
n
133
ARG
133
A
SER
134
n
134
SER
134
A
VAL
135
n
135
VAL
135
A
ASP
136
n
136
ASP
136
A
VAL
137
n
137
VAL
137
A
GLY
138
n
138
GLY
138
A
THR
139
n
139
THR
139
A
TRP
140
n
140
TRP
140
A
ILE
141
n
141
ILE
141
A
ALA
142
n
142
ALA
142
A
GLY
143
n
143
GLY
143
A
VAL
144
n
144
VAL
144
A
GLY
145
n
145
GLY
145
A
TYR
146
n
146
TYR
146
A
ARG
147
n
147
ARG
147
A
PHE
148
n
148
PHE
148
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
THR
6
A
N
THR
6
A
O
LYS
27
A
O
LYS
27
A
N
GLY
22
A
N
GLY
22
A
O
GLU
47
A
O
GLU
47
A
N
THR
44
A
N
THR
44
A
O
GLY
64
A
O
GLY
64
A
N
TYR
71
A
N
TYR
71
A
O
ILE
79
A
O
ILE
79
A
N
VAL
82
A
N
VAL
82
A
O
GLY
110
A
O
GLY
110
A
N
LEU
113
A
N
LEU
113
A
O
PHE
125
A
O
PHE
125
A
N
ILE
132
A
N
ILE
132
A
O
VAL
135
A
O
VAL
135
A
O
ASP
136
A
O
ASP
136
A
N
GLN
15
A
N
GLN
15
1
A
SER
53
-179.61
-73.91
1
A
ASN
74
47.95
27.36
1
A
ASP
75
40.76
28.81
1
A
TRP
76
-98.67
-63.69
1
A
ASN
116
58.79
70.95
1
A
PRO
117
-86.54
34.80
1
A
GLU
119
57.05
-171.56
1
A
ARG
133
15.66
95.14
1
A
SER
134
75.19
-10.36
2
A
ASN
19
47.61
-174.95
2
A
ASP
75
43.64
26.15
2
A
HIS
100
-167.54
-50.68
2
A
ASP
101
-145.39
33.41
2
A
PRO
117
-61.01
-70.79
2
A
MET
118
-79.33
-72.62
2
A
GLU
119
-175.14
-68.78
2
A
ARG
133
15.60
95.11
2
A
SER
134
75.33
-10.87
3
A
ASN
19
69.61
145.36
3
A
SER
53
50.92
97.65
3
A
SER
54
-174.47
-53.25
3
A
ASN
58
-178.94
115.98
3
A
ASN
74
61.59
108.51
3
A
TRP
76
47.55
23.68
3
A
GLU
94
173.91
149.03
3
A
HIS
100
61.82
120.15
3
A
ASN
116
66.73
72.64
3
A
ARG
133
16.68
95.17
3
A
SER
134
73.57
-8.33
4
A
ASN
19
65.62
125.71
4
A
ILE
73
-150.14
51.79
4
A
ASN
74
176.08
173.09
4
A
ALA
77
68.81
103.21
4
A
PRO
117
-73.62
-165.86
4
A
ARG
133
14.87
95.11
4
A
SER
134
75.17
-10.86
5
A
ASN
19
70.53
120.38
5
A
SER
53
-163.05
-67.24
5
A
ASN
74
59.97
-84.62
5
A
GLU
94
174.01
149.13
5
A
HIS
100
41.38
29.95
5
A
PRO
117
-91.43
53.04
5
A
ARG
133
17.14
95.20
5
A
SER
134
76.92
-13.46
6
A
TRP
76
-103.27
-62.67
6
A
GLU
94
175.83
149.30
6
A
PRO
117
-76.37
-167.10
6
A
ARG
133
-47.07
95.25
6
A
SER
134
149.93
-54.24
7
A
ASN
19
64.81
142.10
7
A
ILE
73
-103.04
-72.29
7
A
GLU
94
178.60
149.27
7
A
PRO
117
-70.71
-168.03
7
A
ARG
133
16.69
95.19
7
A
SER
134
75.40
-12.18
8
A
ASN
19
66.61
142.17
8
A
ASN
74
58.25
169.09
8
A
ALA
77
177.60
112.26
8
A
GLU
94
179.96
149.32
8
A
PRO
117
-95.74
-158.74
8
A
ARG
133
14.74
95.03
8
A
SER
134
73.14
-7.60
9
A
SER
53
-175.22
-67.88
9
A
TRP
76
-160.59
-80.66
9
A
ALA
77
177.76
178.85
9
A
HIS
100
46.35
29.19
9
A
THR
102
-143.32
-30.59
9
A
PRO
117
-75.15
-164.71
9
A
ARG
133
16.38
95.27
9
A
SER
134
75.43
-11.65
10
A
ASN
19
-171.40
137.09
10
A
HIS
100
178.95
139.67
10
A
PRO
117
-69.99
-163.43
10
A
ARG
133
13.32
95.25
10
A
SER
134
74.78
-9.66
11
A
ASN
74
58.79
112.45
11
A
HIS
100
-177.06
-63.54
11
A
MET
118
-95.55
-73.47
11
A
GLU
119
-175.31
-65.67
11
A
ARG
133
15.06
95.17
11
A
SER
134
74.45
-9.06
12
A
ASN
19
71.45
141.86
12
A
SER
53
-169.55
-58.23
12
A
GLU
94
-174.68
149.30
12
A
HIS
100
-166.54
-55.05
12
A
ASP
101
-151.37
81.98
12
A
ARG
133
15.11
95.21
12
A
SER
134
74.75
-9.92
13
A
TRP
76
61.08
-84.33
13
A
ALA
77
-178.63
-98.34
13
A
ASN
116
70.28
66.12
13
A
ARG
133
16.49
95.09
13
A
SER
134
73.35
-8.57
14
A
ASN
19
68.00
116.41
14
A
SER
53
-173.67
-67.15
14
A
ALA
77
-55.91
-177.58
14
A
GLU
94
178.98
149.33
14
A
ASN
116
72.89
65.68
14
A
ARG
133
17.05
95.16
14
A
SER
134
74.20
-8.67
15
A
ILE
73
-177.25
-60.49
15
A
TRP
76
57.67
-85.45
15
A
HIS
100
-158.97
-43.78
15
A
PRO
117
-77.31
-165.81
15
A
ARG
133
-45.09
95.02
15
A
SER
134
148.13
-53.95
16
A
ILE
73
80.13
-29.81
16
A
ALA
77
56.67
-173.49
16
A
GLU
94
-179.76
149.31
16
A
PRO
117
-78.24
-167.91
16
A
ARG
133
-45.15
95.14
16
A
SER
134
150.52
-54.05
17
A
ASN
19
-176.85
147.30
17
A
SER
53
-169.49
-66.68
17
A
ALA
77
61.64
92.63
17
A
GLU
94
173.62
149.20
17
A
HIS
100
66.15
-82.72
17
A
PRO
117
-74.85
-168.06
17
A
ARG
133
15.50
95.11
17
A
SER
134
74.04
-8.81
18
A
ASN
19
66.93
135.42
18
A
GLU
94
176.51
149.25
18
A
THR
102
-174.73
-39.94
18
A
ARG
133
15.24
95.10
18
A
SER
134
73.45
-7.53
19
A
ASN
19
46.65
-176.26
19
A
ALA
77
52.99
-172.49
19
A
GLU
94
-178.64
149.25
19
A
MET
118
-95.23
-73.55
19
A
GLU
119
-174.94
-62.91
19
A
ARG
133
14.88
95.11
19
A
SER
134
74.40
-9.14
20
A
ASN
19
68.59
133.32
20
A
SER
53
179.82
-70.00
20
A
GLU
94
174.81
149.34
20
A
HIS
100
60.44
-84.26
20
A
ASN
116
66.31
74.66
20
A
ARG
133
-43.80
94.98
20
A
SER
134
149.70
-51.87
fewest violations, model 1
NMR structure of OmpX in phopspholipid nanodiscs
1
N
N
MEMBRANE PROTEIN
beta barrel, MEMBRANE PROTEIN, Structural Genomics, PSI-Biology, Membrane Protein Structures by Solution NMR, MPSbyNMR
OMPX_ECOLI
UNP
1
24
P0A917
ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTASSGDYNKNQYYGITAGPAYRINDWASIY
GVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF
24
171
2M06
1
148
P0A917
A
1
1
148
9
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
SER
3
A
SER
3
A
GLN
15
A
GLN
15
A
LYS
20
A
LYS
20
A
TYR
30
A
TYR
30
A
GLY
38
A
GLY
38
A
LYS
48
A
LYS
48
A
ASN
60
A
ASN
60
A
ILE
73
A
ILE
73
A
ALA
77
A
ALA
77
A
PHE
90
A
PHE
90
A
ASP
104
A
ASP
104
A
PHE
115
A
PHE
115
A
ALA
122
A
ALA
122
A
ILE
132
A
ILE
132
A
VAL
135
A
VAL
135
A
PHE
148
A
PHE
148
A
SER
3
A
SER
3
A
GLN
15
A
GLN
15