1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kato, K.
Yamaguchi, Y.
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
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
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
To be Published
0353
Solution structure of the a' domain of thermophilic fungal protein disulfide isomerase
10.2210/pdb2djj/pdb
pdb_00002djj
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
13123.905
Protein disulfide-isomerase
5.3.4.1
a' domain
1
man
polymer
PDI
no
no
GPLGSEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQ
GFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA
GPLGSEGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQ
GFPTIKLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA
A
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
Humicola
Escherichia
Escherichia coli
sample
34413
Humicola insolens
469008
Escherichia coli BL21(DE3)
BL21(DE3)
PLASMID
pGEX6P-1
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2006-04-25
1
1
2008-04-30
1
2
2011-07-13
1
3
2022-03-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
2006-04-25
SPRSDE
PDBJ
Y
PDBJ
2006-04-04
REL
structures with the lowest energy
100
10
3D_13C-separated_NOESY
3D_15N-separated_NOESY
2D NOESY
1H-15N HSQC
0.16
6
1
atm
310
K
distance geometry simulated annealing
1
lowest energy
1.0mM protein disulfide isomerase a' domain U-15N,13C; 10mM sodium phosphate buffer, 100mM KCl, 10mM ditiothreitol; 90% H2O, 10% D2O
90% H2O/10% D2O
1.0mM protein disulfide isomerase a' domain; 10mM sodium phosphate buffer, 100mM KCl, 10mM ditiothreitol; 99% D2O
99% D2O
0.3mM protein disulfide isomerase a' domain U-15N; 10mM sodium phosphate buffer, 100mM KCl, 10mM ditiothreitol, 10mg/ml Pf1 phage; 90% H2O, 10% D2O
90% H2O/10% D2O
collection
XwinNMR
2.6
collection
Delta
4.3.3
processing
XwinNMR
2.6
Goddard and Kneller
data analysis
Sparky
3.1
Guntert
structure solution
CYANA
2.1
refinement
CNS
1.1
920
JEOL
ECA
800
Bruker
DRX
GLY
1
n
1
GLY
1
A
PRO
2
n
2
PRO
2
A
LEU
3
n
3
LEU
3
A
GLY
4
n
4
GLY
4
A
SER
5
n
5
SER
5
A
GLU
6
n
6
GLU
6
A
GLY
7
n
7
GLY
7
A
PRO
8
n
8
PRO
8
A
VAL
9
n
9
VAL
9
A
THR
10
n
10
THR
10
A
VAL
11
n
11
VAL
11
A
VAL
12
n
12
VAL
12
A
VAL
13
n
13
VAL
13
A
ALA
14
n
14
ALA
14
A
LYS
15
n
15
LYS
15
A
ASN
16
n
16
ASN
16
A
TYR
17
n
17
TYR
17
A
ASN
18
n
18
ASN
18
A
GLU
19
n
19
GLU
19
A
ILE
20
n
20
ILE
20
A
VAL
21
n
21
VAL
21
A
LEU
22
n
22
LEU
22
A
ASP
23
n
23
ASP
23
A
ASP
24
n
24
ASP
24
A
THR
25
n
25
THR
25
A
LYS
26
n
26
LYS
26
A
ASP
27
n
27
ASP
27
A
VAL
28
n
28
VAL
28
A
LEU
29
n
29
LEU
29
A
ILE
30
n
30
ILE
30
A
GLU
31
n
31
GLU
31
A
PHE
32
n
32
PHE
32
A
TYR
33
n
33
TYR
33
A
ALA
34
n
34
ALA
34
A
PRO
35
n
35
PRO
35
A
TRP
36
n
36
TRP
36
A
CYS
37
n
37
CYS
37
A
GLY
38
n
38
GLY
38
A
HIS
39
n
39
HIS
39
A
CYS
40
n
40
CYS
40
A
LYS
41
n
41
LYS
41
A
ALA
42
n
42
ALA
42
A
LEU
43
n
43
LEU
43
A
ALA
44
n
44
ALA
44
A
PRO
45
n
45
PRO
45
A
LYS
46
n
46
LYS
46
A
TYR
47
n
47
TYR
47
A
GLU
48
n
48
GLU
48
A
GLU
49
n
49
GLU
49
A
LEU
50
n
50
LEU
50
A
GLY
51
n
51
GLY
51
A
ALA
52
n
52
ALA
52
A
LEU
53
n
53
LEU
53
A
TYR
54
n
54
TYR
54
A
ALA
55
n
55
ALA
55
A
LYS
56
n
56
LYS
56
A
SER
57
n
57
SER
57
A
GLU
58
n
58
GLU
58
A
PHE
59
n
59
PHE
59
A
LYS
60
n
60
LYS
60
A
ASP
61
n
61
ASP
61
A
ARG
62
n
62
ARG
62
A
VAL
63
n
63
VAL
63
A
VAL
64
n
64
VAL
64
A
ILE
65
n
65
ILE
65
A
ALA
66
n
66
ALA
66
A
LYS
67
n
67
LYS
67
A
VAL
68
n
68
VAL
68
A
ASP
69
n
69
ASP
69
A
ALA
70
n
70
ALA
70
A
THR
71
n
71
THR
71
A
ALA
72
n
72
ALA
72
A
ASN
73
n
73
ASN
73
A
ASP
74
n
74
ASP
74
A
VAL
75
n
75
VAL
75
A
PRO
76
n
76
PRO
76
A
ASP
77
n
77
ASP
77
A
GLU
78
n
78
GLU
78
A
ILE
79
n
79
ILE
79
A
GLN
80
n
80
GLN
80
A
GLY
81
n
81
GLY
81
A
PHE
82
n
82
PHE
82
A
PRO
83
n
83
PRO
83
A
THR
84
n
84
THR
84
A
ILE
85
n
85
ILE
85
A
LYS
86
n
86
LYS
86
A
LEU
87
n
87
LEU
87
A
TYR
88
n
88
TYR
88
A
PRO
89
n
89
PRO
89
A
ALA
90
n
90
ALA
90
A
GLY
91
n
91
GLY
91
A
ALA
92
n
92
ALA
92
A
LYS
93
n
93
LYS
93
A
GLY
94
n
94
GLY
94
A
GLN
95
n
95
GLN
95
A
PRO
96
n
96
PRO
96
A
VAL
97
n
97
VAL
97
A
THR
98
n
98
THR
98
A
TYR
99
n
99
TYR
99
A
SER
100
n
100
SER
100
A
GLY
101
n
101
GLY
101
A
SER
102
n
102
SER
102
A
ARG
103
n
103
ARG
103
A
THR
104
n
104
THR
104
A
VAL
105
n
105
VAL
105
A
GLU
106
n
106
GLU
106
A
ASP
107
n
107
ASP
107
A
LEU
108
n
108
LEU
108
A
ILE
109
n
109
ILE
109
A
LYS
110
n
110
LYS
110
A
PHE
111
n
111
PHE
111
A
ILE
112
n
112
ILE
112
A
ALA
113
n
113
ALA
113
A
GLU
114
n
114
GLU
114
A
ASN
115
n
115
ASN
115
A
GLY
116
n
116
GLY
116
A
LYS
117
n
117
LYS
117
A
TYR
118
n
118
TYR
118
A
LYS
119
n
119
LYS
119
A
ALA
120
n
120
ALA
120
A
ALA
121
n
121
ALA
121
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
10
A
N
THR
10
A
O
LYS
67
A
O
LYS
67
A
O
VAL
64
A
O
VAL
64
A
N
LEU
29
A
N
LEU
29
A
N
ILE
30
A
N
ILE
30
A
O
LYS
86
A
O
LYS
86
1
A
A
O
H
PHE
ASN
111
115
1.55
2
A
A
O
H
PHE
ASN
111
115
1.57
3
A
A
O
H
PHE
ASN
111
115
1.52
3
A
A
O
H
ASN
GLU
16
19
1.54
4
A
A
O
H
PHE
ASN
111
115
1.59
4
A
A
O
H
SER
THR
102
104
1.60
5
A
A
O
H
ASN
GLU
16
19
1.55
5
A
A
O
H
PHE
ASN
111
115
1.59
6
A
A
O
H
PHE
ASN
111
115
1.53
7
A
A
O
H
PHE
ASN
111
115
1.53
7
A
A
O
H
ASN
GLU
16
19
1.60
8
A
A
O
H
PHE
ASN
111
115
1.45
8
A
A
O
H
ASN
GLU
16
19
1.59
9
A
A
O
H
PHE
ASN
111
115
1.58
9
A
A
O
H
ASN
GLU
16
19
1.60
10
A
A
O
H
PHE
ASN
111
115
1.56
10
A
A
O
H
ASN
GLU
16
19
1.58
1
A
SER
5
-173.72
-75.75
1
A
LYS
56
-155.22
11.26
1
A
SER
57
-109.81
-102.66
1
A
PHE
59
-152.37
21.83
1
A
ARG
62
-125.78
-142.36
1
A
PRO
96
-44.09
-176.24
1
A
ARG
103
-106.01
52.47
1
A
PHE
111
-65.17
-77.62
1
A
ALA
120
-62.94
98.75
2
A
PRO
2
-52.19
175.93
2
A
LEU
3
-154.65
-52.61
2
A
LYS
56
-146.03
-43.38
2
A
SER
57
-61.09
-149.99
2
A
ARG
62
-85.03
-145.63
2
A
LYS
86
-163.16
119.03
2
A
PRO
89
-55.03
177.93
2
A
ALA
90
-95.79
54.38
2
A
PRO
96
-39.82
172.62
2
A
SER
102
-159.86
-40.45
2
A
PHE
111
-65.49
-77.47
3
A
GLU
6
-178.81
111.71
3
A
LYS
56
-143.13
-45.01
3
A
SER
57
-59.95
-153.10
3
A
ARG
62
-121.64
-147.06
3
A
VAL
63
-48.86
107.45
3
A
GLU
78
-66.78
95.69
3
A
PRO
83
-71.52
-168.00
3
A
PRO
89
-51.74
175.52
3
A
ALA
90
-102.51
53.04
3
A
ALA
92
-102.21
-81.14
3
A
GLN
95
-144.31
57.47
3
A
PRO
96
-44.77
177.05
3
A
ARG
103
-106.17
51.53
3
A
PHE
111
-64.03
-75.93
4
A
LEU
3
61.93
116.29
4
A
GLU
6
-170.95
-173.74
4
A
LYS
56
-139.80
-42.40
4
A
SER
57
-57.36
-159.89
4
A
ARG
62
-82.75
-143.66
4
A
PRO
89
-56.38
177.83
4
A
ALA
90
-95.17
54.11
4
A
PRO
96
-39.03
175.06
4
A
SER
102
179.83
106.56
4
A
ARG
103
-69.00
54.51
4
A
PHE
111
-64.74
-77.39
5
A
VAL
11
-67.09
92.48
5
A
GLU
19
-121.00
-53.75
5
A
LYS
56
-145.51
-42.49
5
A
SER
57
-57.69
-156.12
5
A
GLU
58
-79.33
23.77
5
A
PHE
59
-149.05
26.23
5
A
ARG
62
-85.28
-142.61
5
A
ASP
74
-50.35
102.18
5
A
PHE
82
174.60
140.93
5
A
PRO
83
-74.69
-161.17
5
A
PRO
89
-55.60
176.79
5
A
ALA
90
-94.57
53.75
5
A
PRO
96
-41.89
-173.20
5
A
PHE
111
-65.30
-78.26
6
A
PRO
2
-69.98
63.13
6
A
SER
5
-74.74
-168.29
6
A
LYS
56
-140.82
-40.60
6
A
SER
57
-57.16
-160.63
6
A
ARG
62
-113.38
-141.33
6
A
PRO
83
-79.60
-164.64
6
A
ALA
90
-94.62
53.33
6
A
ALA
92
-101.57
-78.45
6
A
GLN
95
-149.82
59.34
6
A
PRO
96
-42.99
-175.96
6
A
PHE
111
-66.00
-77.30
7
A
TYR
33
-161.19
-167.71
7
A
LYS
56
-149.35
-43.20
7
A
SER
57
-60.71
-151.43
7
A
GLU
58
-79.45
20.38
7
A
ARG
62
-81.89
-136.12
7
A
VAL
63
-46.22
152.65
7
A
PRO
89
-56.73
177.02
7
A
ALA
90
-95.56
53.74
7
A
PRO
96
-42.22
176.41
7
A
ARG
103
47.65
27.24
7
A
PHE
111
-65.23
-77.98
8
A
SER
5
-117.11
-80.25
8
A
GLU
6
177.57
44.13
8
A
VAL
9
-62.60
-176.37
8
A
VAL
11
-63.07
84.57
8
A
LYS
56
-146.39
-42.35
8
A
SER
57
-60.41
-147.12
8
A
PHE
59
-140.07
17.14
8
A
ARG
62
-115.21
-143.23
8
A
PRO
83
-73.73
-168.94
8
A
PRO
89
-57.43
177.32
8
A
ALA
90
-96.60
53.88
8
A
PRO
96
-46.38
-179.70
8
A
SER
102
-153.43
-41.04
8
A
PHE
111
-65.25
-78.40
9
A
CYS
37
-68.09
96.24
9
A
LYS
56
-149.77
-43.69
9
A
SER
57
-61.80
-146.91
9
A
ARG
62
-85.07
-145.87
9
A
THR
71
-160.93
-21.35
9
A
ASN
73
-113.98
-157.01
9
A
PRO
89
-55.55
179.41
9
A
ALA
90
-96.77
53.82
9
A
PRO
96
-40.82
175.36
9
A
SER
102
-177.53
111.64
9
A
PHE
111
-65.11
-77.71
10
A
SER
5
-176.08
-58.12
10
A
GLU
6
61.42
110.87
10
A
THR
10
-61.61
82.05
10
A
LYS
56
-143.41
-43.50
10
A
SER
57
-59.20
-150.14
10
A
ARG
62
-84.56
-145.65
10
A
ALA
90
-90.83
55.19
10
A
PRO
96
-39.93
-179.14
10
A
SER
102
-158.32
-35.77
10
A
ARG
103
70.45
40.77
10
A
PHE
111
-66.05
-78.70
Solution structure of the a' domain of thermophilic fungal protein disulfide isomerase
1
N
N
A
HIS
39
A
HIS
39
HELX_P
A
ALA
55
A
ALA
55
1
1
17
A
THR
104
A
THR
104
HELX_P
A
ASN
115
A
ASN
115
1
2
12
ISOMERASE
thioredoxin fold, ISOMERASE
A
PHE
82
A
PHE
82
1
A
PRO
83
A
PRO
83
-0.18
A
PHE
82
A
PHE
82
2
A
PRO
83
A
PRO
83
-0.02
A
PHE
82
A
PHE
82
3
A
PRO
83
A
PRO
83
0.29
A
PHE
82
A
PHE
82
4
A
PRO
83
A
PRO
83
0.12
A
PHE
82
A
PHE
82
5
A
PRO
83
A
PRO
83
-0.04
A
PHE
82
A
PHE
82
6
A
PRO
83
A
PRO
83
-0.20
A
PHE
82
A
PHE
82
7
A
PRO
83
A
PRO
83
0.02
A
PHE
82
A
PHE
82
8
A
PRO
83
A
PRO
83
0.21
A
PHE
82
A
PHE
82
9
A
PRO
83
A
PRO
83
0.14
A
PHE
82
A
PHE
82
10
A
PRO
83
A
PRO
83
0.15
PDI_HUMIN
UNP
1
354
P55059
EGPVTVVVAKNYNEIVLDDTKDVLIEFYAPWCGHCKALAPKYEELGALYAKSEFKDRVVIAKVDATANDVPDEIQGFPTI
KLYPAGAKGQPVTYSGSRTVEDLIKFIAENGKYKAA
354
469
2DJJ
6
121
P55059
A
1
6
121
1
cloning artifact
GLY
1
2DJJ
A
P55059
UNP
1
1
cloning artifact
PRO
2
2DJJ
A
P55059
UNP
2
1
cloning artifact
LEU
3
2DJJ
A
P55059
UNP
3
1
cloning artifact
GLY
4
2DJJ
A
P55059
UNP
4
1
cloning artifact
SER
5
2DJJ
A
P55059
UNP
5
4
parallel
parallel
anti-parallel
A
THR
10
A
THR
10
A
VAL
11
A
VAL
11
A
VAL
64
A
VAL
64
A
ASP
69
A
ASP
69
A
VAL
28
A
VAL
28
A
TYR
33
A
TYR
33
A
THR
84
A
THR
84
A
TYR
88
A
TYR
88