1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Volpon, L.
Lievre, C.
Osborne, M.J.
Gandhi, S.
Iannuzzi, P.
Larocque, R.
Matte, A.
Cygler, M.
Gehring, K.
Ekiel, I.
Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C3 H7 N O2 S
121.158
y
CYSTEINE
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
J.Bacteriol.
JOBAAY
0767
0021-9193
185
4204
4210
10.1128/JB.185.14.4204-4210.2003
12837795
The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding.
2003
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
x-ray
1
1.0
8416.737
orf, hypothetical protein
1
man
polymer
no
no
GSMIHRMSNMATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA
GSMIHRMSNMATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA
A
YBCJ_ECOLI
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
Escherichia
Escherichia coli
K12
Escherichia
Escherichia coli
sample
ybcJ
83333
Escherichia coli
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PLASMID
pET20b
Montreal-Kingston Bacterial Structural Genomics Initiative
BSGI
repository
Initial release
Version format compliance
Source and taxonomy
Version format compliance
1
0
2003-11-25
1
1
2008-04-29
1
2
2011-07-13
2003-11-25
SPRSDE
Y
RCSB
Y
RCSB
2003-05-12
REL
REL
This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques.
structures with the least restraint violations,structures with the lowest energy
60
20
2D NOESY
DQF-COSY
HNHA
3D_15N-separated_NOESY
IPAP-HSQC
50mM Phosphate, 300mM NaCl
6.8
ambient
313
K
The structures are based on a total of 1205 restraints, 1011 are NOE-derived distance constraints, 89 dihedral angle restraints, 54 distance restraints from hydrogen bonds (27 hydrogen bonds), and 51 15N-1H residual dipolar couplings.
simulated annealing
7
closest to the average
4-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8
90% H2O/10% D2O
4-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8,
8mg/mL of Pf1 phage
90% H2O/10% D2O
Delsuc
processing
GIFA
4.31
Bruker
collection
XWINNMR
2.1
Bartels
data analysis
XEASY
1.3.13
Bax
refinement
TALOS
2003.027.13.05
Nilges
refinement
ARIA
1.1
Brunger
refinement
CNS
1.1
500
Bruker
DRX
600
Bruker
Avance
GLY
1
n
1
GLY
1
A
SER
2
n
2
SER
2
A
MET
3
n
3
MET
3
A
ILE
4
n
4
ILE
4
A
HIS
5
n
5
HIS
5
A
ARG
6
n
6
ARG
6
A
MET
7
n
7
MET
7
A
SER
8
n
8
SER
8
A
ASN
9
n
9
ASN
9
A
MET
10
n
10
MET
10
A
ALA
11
n
11
ALA
11
A
THR
12
n
12
THR
12
A
PHE
13
n
13
PHE
13
A
SER
14
n
14
SER
14
A
LEU
15
n
15
LEU
15
A
GLY
16
n
16
GLY
16
A
LYS
17
n
17
LYS
17
A
HIS
18
n
18
HIS
18
A
PRO
19
n
19
PRO
19
A
HIS
20
n
20
HIS
20
A
VAL
21
n
21
VAL
21
A
GLU
22
n
22
GLU
22
A
LEU
23
n
23
LEU
23
A
CYS
24
n
24
CYS
24
A
ASP
25
n
25
ASP
25
A
LEU
26
n
26
LEU
26
A
LEU
27
n
27
LEU
27
A
LYS
28
n
28
LYS
28
A
LEU
29
n
29
LEU
29
A
GLU
30
n
30
GLU
30
A
GLY
31
n
31
GLY
31
A
TRP
32
n
32
TRP
32
A
SER
33
n
33
SER
33
A
GLU
34
n
34
GLU
34
A
SER
35
n
35
SER
35
A
GLY
36
n
36
GLY
36
A
ALA
37
n
37
ALA
37
A
GLN
38
n
38
GLN
38
A
ALA
39
n
39
ALA
39
A
LYS
40
n
40
LYS
40
A
ILE
41
n
41
ILE
41
A
ALA
42
n
42
ALA
42
A
ILE
43
n
43
ILE
43
A
ALA
44
n
44
ALA
44
A
GLU
45
n
45
GLU
45
A
GLY
46
n
46
GLY
46
A
GLN
47
n
47
GLN
47
A
VAL
48
n
48
VAL
48
A
LYS
49
n
49
LYS
49
A
VAL
50
n
50
VAL
50
A
ASP
51
n
51
ASP
51
A
GLY
52
n
52
GLY
52
A
ALA
53
n
53
ALA
53
A
VAL
54
n
54
VAL
54
A
GLU
55
n
55
GLU
55
A
THR
56
n
56
THR
56
A
ARG
57
n
57
ARG
57
A
LYS
58
n
58
LYS
58
A
ARG
59
n
59
ARG
59
A
CYS
60
n
60
CYS
60
A
LYS
61
n
61
LYS
61
A
ILE
62
n
62
ILE
62
A
VAL
63
n
63
VAL
63
A
ALA
64
n
64
ALA
64
A
GLY
65
n
65
GLY
65
A
GLN
66
n
66
GLN
66
A
THR
67
n
67
THR
67
A
VAL
68
n
68
VAL
68
A
SER
69
n
69
SER
69
A
PHE
70
n
70
PHE
70
A
ALA
71
n
71
ALA
71
A
GLY
72
n
72
GLY
72
A
HIS
73
n
73
HIS
73
A
SER
74
n
74
SER
74
A
VAL
75
n
75
VAL
75
A
GLN
76
n
76
GLN
76
A
VAL
77
n
77
VAL
77
A
VAL
78
n
78
VAL
78
A
ALA
79
n
79
ALA
79
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
PHE
13
A
N
PHE
13
A
O
GLN
76
A
O
GLN
76
A
O
VAL
77
A
O
VAL
77
A
N
GLN
66
A
N
GLN
66
A
O
SER
69
A
O
SER
69
A
N
LYS
49
A
N
LYS
49
3
A
A
O
H
VAL
ALA
50
53
1.57
4
A
A
O
H
GLN
VAL
66
77
1.59
4
A
A
H
O
VAL
VAL
68
75
1.60
5
A
A
O
H
VAL
ALA
50
53
1.56
5
A
A
H
O
PHE
GLN
13
76
1.59
5
A
A
O
H
PHE
HIS
70
73
1.59
6
A
A
O
H
PHE
HIS
70
73
1.58
6
A
A
O
H
VAL
ALA
50
53
1.59
7
A
A
O
H
VAL
ALA
50
53
1.55
8
A
A
O
H
VAL
ALA
50
53
1.56
10
A
A
O
H
PHE
HIS
70
73
1.56
10
A
A
O
H
VAL
ALA
50
53
1.59
12
A
A
O
H
VAL
ALA
50
53
1.53
14
A
A
O
H
VAL
ALA
50
53
1.53
16
A
A
O
H
VAL
ALA
50
53
1.56
19
A
A
O
H
VAL
ALA
50
53
1.58
1
A
SER
2
-151.58
80.29
1
A
MET
3
-168.58
72.91
1
A
MET
7
74.43
-31.32
1
A
SER
8
67.72
115.99
1
A
LYS
17
-143.86
57.40
1
A
HIS
20
171.38
-170.36
1
A
GLN
38
-54.91
-74.69
1
A
ALA
42
-74.11
-79.14
1
A
GLN
47
-46.33
-14.62
1
A
VAL
48
-74.92
-88.21
1
A
LYS
49
-172.84
128.87
1
A
ASP
51
-55.66
85.91
1
A
GLU
55
-106.94
-151.39
1
A
THR
56
-166.96
57.30
1
A
ALA
64
74.40
-150.39
1
A
ALA
71
46.67
-87.01
2
A
SER
2
63.43
103.26
2
A
ARG
6
61.65
94.51
2
A
LYS
17
-151.06
56.62
2
A
HIS
20
163.01
-164.32
2
A
ALA
42
-72.21
-79.81
2
A
ALA
44
-63.09
-72.18
2
A
GLN
47
-47.96
-9.52
2
A
VAL
48
-74.66
-90.67
2
A
LYS
49
-167.02
119.37
2
A
ASP
51
-44.70
98.20
2
A
ALA
64
74.48
-155.01
2
A
ALA
71
48.72
-85.03
3
A
SER
2
65.68
-171.44
3
A
ILE
4
60.36
117.89
3
A
HIS
5
-172.82
-60.45
3
A
ARG
6
58.40
167.66
3
A
MET
7
58.28
-172.30
3
A
SER
8
67.55
161.59
3
A
ASN
9
-165.46
-62.38
3
A
HIS
20
168.14
-174.60
3
A
LEU
23
-38.08
-39.28
3
A
GLN
38
-61.11
-79.42
3
A
ALA
42
-74.40
-79.09
3
A
GLN
47
-48.26
-10.88
3
A
VAL
48
-75.33
-96.66
3
A
ASP
51
-44.79
97.05
3
A
THR
56
-147.29
46.19
3
A
ALA
64
72.69
-151.27
3
A
ALA
71
47.55
-85.85
4
A
HIS
5
64.50
139.43
4
A
ARG
6
-168.66
71.46
4
A
MET
7
-99.48
-62.90
4
A
LYS
17
-149.84
54.72
4
A
HIS
20
162.75
-165.65
4
A
LEU
23
-39.82
-36.45
4
A
TRP
32
-64.63
-73.52
4
A
ALA
42
-73.05
-76.40
4
A
GLN
47
-47.57
-11.58
4
A
VAL
48
-75.32
-99.61
4
A
ASP
51
-44.03
87.01
4
A
THR
56
-164.00
30.27
4
A
LYS
61
-103.74
78.75
4
A
ALA
64
78.76
-138.45
4
A
PHE
70
-175.68
130.38
5
A
HIS
5
-138.16
-59.50
5
A
ASN
9
-142.98
-37.84
5
A
HIS
20
172.85
-163.79
5
A
GLN
38
-55.25
-71.11
5
A
ALA
42
-69.64
-77.75
5
A
ALA
44
-57.74
-71.19
5
A
GLN
47
-49.15
-8.17
5
A
VAL
48
-75.33
-98.71
5
A
ASP
51
-44.96
102.48
5
A
THR
56
-142.89
47.67
5
A
ALA
64
71.19
-136.52
5
A
ALA
71
38.20
30.01
6
A
MET
3
-67.27
-179.52
6
A
ILE
4
-147.17
-32.16
6
A
MET
7
64.49
74.09
6
A
LEU
15
-142.30
-36.03
6
A
HIS
20
174.98
-176.37
6
A
GLN
38
-52.52
-76.34
6
A
ALA
42
-75.92
-77.35
6
A
GLU
45
-29.81
-44.13
6
A
GLN
47
-48.64
-12.94
6
A
VAL
48
-75.06
-98.17
6
A
ASP
51
-44.72
101.29
6
A
GLU
55
-102.56
-166.25
6
A
THR
56
-145.80
37.99
6
A
LYS
61
-69.48
99.09
6
A
ALA
64
72.31
-149.73
7
A
SER
2
58.16
175.77
7
A
MET
3
-138.25
-38.98
7
A
SER
8
-133.97
-47.63
7
A
HIS
20
164.64
-166.98
7
A
GLN
38
-60.48
-74.57
7
A
ALA
42
-70.68
-80.68
7
A
ALA
44
-61.33
-72.31
7
A
GLN
47
-48.49
-9.35
7
A
VAL
48
-74.66
-89.26
7
A
LYS
49
-170.31
120.97
7
A
ASP
51
-44.99
98.68
7
A
THR
56
-150.85
36.81
7
A
ALA
64
77.96
-149.20
7
A
ALA
71
51.99
-85.12
8
A
MET
3
-154.90
29.70
8
A
HIS
20
173.86
-173.67
8
A
ALA
37
-144.46
-2.58
8
A
GLN
38
-60.13
-74.71
8
A
ALA
42
-65.38
-78.68
8
A
ALA
44
-61.21
-71.68
8
A
GLN
47
-50.24
-9.46
8
A
VAL
48
-75.45
-101.24
8
A
ASP
51
-48.60
95.74
8
A
THR
56
-143.95
41.40
8
A
ALA
64
72.27
-133.77
8
A
PHE
70
-176.13
137.21
9
A
SER
2
-79.14
-164.89
9
A
ILE
4
-133.72
-63.23
9
A
SER
8
-169.74
119.61
9
A
ASN
9
-122.71
-71.32
9
A
LYS
17
-173.40
53.47
9
A
HIS
20
167.15
-173.57
9
A
GLN
38
-52.52
-73.71
9
A
ALA
42
-75.29
-76.56
9
A
GLU
45
-28.31
-47.75
9
A
GLN
47
-44.57
-16.21
9
A
VAL
48
-76.01
-95.43
9
A
ASP
51
-43.62
99.71
9
A
GLU
55
-100.42
-162.72
9
A
THR
56
-144.43
53.11
9
A
ALA
64
72.58
-138.17
9
A
ALA
71
40.82
28.23
10
A
SER
2
58.60
86.47
10
A
MET
3
58.70
170.78
10
A
ARG
6
-170.60
127.77
10
A
HIS
20
167.94
-168.50
10
A
ALA
37
-148.88
-15.32
10
A
GLN
38
-54.29
-77.31
10
A
ALA
42
-74.92
-77.67
10
A
GLN
47
-48.82
-9.37
10
A
VAL
48
-75.02
-97.28
10
A
ASP
51
-44.67
99.95
10
A
THR
56
-158.62
42.77
10
A
LYS
61
-110.07
74.71
10
A
ALA
64
78.18
-144.64
10
A
ALA
71
36.47
32.95
11
A
MET
3
56.66
-179.73
11
A
ASN
9
59.08
176.34
11
A
LYS
17
-143.58
41.87
11
A
HIS
20
166.08
-163.96
11
A
GLN
38
-60.91
-76.46
11
A
ALA
42
-71.81
-78.33
11
A
ALA
44
-63.50
-72.23
11
A
GLN
47
-46.52
-10.42
11
A
VAL
48
-74.90
-92.86
11
A
ASP
51
-44.05
101.75
11
A
GLU
55
-101.14
-164.41
11
A
THR
56
-153.18
45.15
11
A
ALA
64
76.52
-143.14
11
A
ALA
71
49.52
-85.47
12
A
SER
2
-131.60
-65.18
12
A
MET
3
66.33
-73.50
12
A
ALA
11
-67.25
99.80
12
A
HIS
20
177.94
-179.72
12
A
LEU
23
-39.70
-38.02
12
A
GLN
38
-59.30
-77.95
12
A
ALA
42
-72.68
-79.69
12
A
ALA
44
-61.00
-72.20
12
A
GLN
47
-48.90
-11.55
12
A
VAL
48
-75.00
-90.92
12
A
ASP
51
-45.29
97.68
12
A
ALA
64
76.22
-150.66
12
A
ALA
71
49.52
-85.46
13
A
ARG
6
-164.95
106.05
13
A
SER
8
-148.96
-60.22
13
A
HIS
20
164.38
-173.70
13
A
GLN
38
-59.74
-76.56
13
A
ALA
42
-69.07
-77.69
13
A
GLN
47
-44.50
-15.86
13
A
VAL
48
-75.05
-91.70
13
A
LYS
49
-171.18
136.88
13
A
ASP
51
-60.61
77.23
13
A
THR
56
-108.66
50.12
13
A
ALA
64
66.21
-150.17
13
A
ALA
71
38.01
30.00
14
A
ALA
11
-64.14
84.70
14
A
LEU
15
-131.49
-37.99
14
A
HIS
20
177.05
178.17
14
A
GLN
38
-53.07
-70.38
14
A
ALA
42
-73.29
-78.92
14
A
GLN
47
-45.63
-15.44
14
A
VAL
48
-74.92
-91.41
14
A
LYS
49
-175.74
130.13
14
A
ASP
51
-44.85
99.21
14
A
THR
56
-142.45
37.74
14
A
ALA
64
76.96
-147.94
14
A
ALA
71
51.08
-81.98
15
A
ILE
4
35.52
93.92
15
A
ARG
6
-147.08
31.58
15
A
ASN
9
-153.13
-36.67
15
A
LYS
17
-175.44
52.19
15
A
HIS
20
165.69
-164.71
15
A
GLN
38
-54.36
-70.33
15
A
ALA
42
-70.75
-79.43
15
A
GLN
47
-46.49
-12.59
15
A
VAL
48
-74.99
-89.32
15
A
ASP
51
-43.89
90.27
15
A
THR
56
-165.24
31.06
15
A
ALA
64
74.88
-148.89
15
A
ALA
71
48.04
-81.38
16
A
SER
2
-153.50
-57.78
16
A
MET
3
62.88
166.54
16
A
HIS
5
-142.55
-16.48
16
A
SER
8
59.83
-175.14
16
A
MET
10
-66.15
96.52
16
A
LYS
17
-148.83
53.62
16
A
HIS
20
170.91
-166.67
16
A
GLN
38
-55.51
-76.06
16
A
ALA
42
-69.62
-78.67
16
A
GLN
47
-47.50
-12.07
16
A
VAL
48
-74.96
-90.83
16
A
ASP
51
-44.68
96.10
16
A
GLU
55
-102.16
-168.64
16
A
THR
56
-151.66
44.12
16
A
ALA
64
78.33
-150.52
16
A
ALA
71
38.29
31.60
17
A
HIS
5
-90.56
-83.48
17
A
MET
7
65.44
88.87
17
A
LYS
17
-174.02
71.85
17
A
HIS
20
170.68
-178.22
17
A
TRP
32
-72.81
-70.49
17
A
GLN
38
-58.45
-72.60
17
A
ALA
42
-76.00
-77.91
17
A
GLU
45
-35.90
-35.60
17
A
GLN
47
-39.93
-18.96
17
A
VAL
48
-75.34
-85.74
17
A
LYS
49
-176.56
130.55
17
A
ASP
51
-65.96
70.65
17
A
THR
56
-99.65
58.23
17
A
LYS
61
-68.61
86.90
17
A
ALA
64
75.26
-154.38
17
A
ALA
71
46.13
-87.10
18
A
HIS
5
-142.31
34.60
18
A
SER
8
59.92
170.93
18
A
ASN
9
83.33
-47.53
18
A
LYS
17
-143.10
43.65
18
A
HIS
20
159.62
-165.38
18
A
GLN
38
-52.25
-75.01
18
A
ALA
42
-66.56
-78.97
18
A
GLN
47
-49.84
-8.57
18
A
VAL
48
-74.87
-90.15
18
A
LYS
49
-171.18
133.97
18
A
ASP
51
-63.53
79.83
18
A
GLU
55
-104.71
-150.46
18
A
THR
56
-169.89
67.40
18
A
ALA
64
81.09
-154.29
18
A
PHE
70
-128.48
-86.24
19
A
MET
3
-163.90
72.85
19
A
HIS
5
71.57
96.19
19
A
ARG
6
59.10
110.63
19
A
LYS
17
-171.44
39.99
19
A
HIS
20
172.71
-172.14
19
A
GLN
38
-54.61
-71.83
19
A
ALA
42
-67.72
-79.34
19
A
GLN
47
-48.06
-12.84
19
A
VAL
48
-75.02
-93.63
19
A
ASP
51
-45.07
100.47
19
A
THR
56
-140.83
32.59
19
A
ALA
64
74.98
-143.51
19
A
ALA
71
49.78
-83.47
20
A
HIS
5
-168.68
-169.97
20
A
HIS
20
178.51
-174.05
20
A
ALA
42
-67.84
-78.51
20
A
GLN
47
-43.69
-19.54
20
A
VAL
48
-75.85
-85.05
20
A
LYS
49
-170.36
133.17
20
A
ASP
51
-48.74
91.25
20
A
THR
56
-92.88
46.84
20
A
ALA
64
72.34
-155.50
20
A
ALA
71
47.21
-85.50
orf, hypothetical protein
THE SOLUTION STRUCTURE OF YBCJ FROM E. COLI REVEALS A RECENTLY DISCOVERED ALFAL MOTIF INVOLVED IN RNA-BINDING
1
N
N
A
GLU
22
A
GLU
22
HELX_P
A
GLY
31
A
GLY
31
1
1
10
A
LYS
40
A
LYS
40
HELX_P
A
VAL
48
A
VAL
48
1
2
9
RNA BINDING PROTEIN
alfaL motif, RNA-binding protein, E.coli, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Structural Genomics, RNA BINDING PROTEIN
YBCJ_ECOLI
UNP
1
1
P0AAS7
MIHRMSNMATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA
1
77
1P9K
3
79
P0AAS7
A
1
3
79
1
CLONING ARTIFACT
GLY
1
1P9K
A
P0AAS7
UNP
1
1
CLONING ARTIFACT
SER
2
1P9K
A
P0AAS7
UNP
2
4
parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
12
A
SER
14
A
SER
14
A
HIS
73
A
HIS
73
A
VAL
78
A
VAL
78
A
GLN
66
A
GLN
66
A
PHE
70
A
PHE
70
A
LYS
49
A
LYS
49
A
VAL
50
A
VAL
50
1
P 1