1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gorbatyuk, V.Y.
Tsai, C.K.
Chang, C.F.
Huang, T.H.
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
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.Biol.Chem.
JBCHA3
0071
0021-9258
279
5772
5780
10.1074/jbc.M311233200
14645226
Effect of N-terminal and Met23 Mutations on the Structure and Dynamics of Onconase
2004
10.2210/pdb1pu3/pdb
pdb_00001pu3
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
1
1.0
11975.836
P-30 protein
3.1.27.-
M23L
1
man
polymer
Onconase
no
no
MQDWLTFQKKHITNTRDVDCDNILSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKL
KKSTNKFCVTCENQAPVHFVGVGSC
MQDWLTFQKKHITNTRDVDCDNILSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKL
KKSTNKFCVTCENQAPVHFVGVGSC
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
northern leopard frog
Rana
Escherichia
Escherichia coli
sample
8404
Rana pipiens
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
pET-11d
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2004-03-16
1
1
2008-04-29
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
1H,13C,15N chemical shifts assignments of the same protein
HNHA coupling constants of the same protein
X-ray crystal structure of the native onconase
RCSB
Y
RCSB
2003-06-24
REL
REL
structures with the lowest energy
100
20
HNHA
3D_15N-separated_NOESY
3D_13C-separated_NOESY
2D TOCSY
2D NOESY
0.3
4.1
ambient
310
K
the structures are based on a total of 1802 restraints, 1550 are NOE-derived
distance constraints, 4 disulfide bonds, 150 dihedral angle restraints, 98 distance restraints
from hydrogen bonds.
simulated annealing, matrix relaxation, torsion angle dymanics
1
minimized average structure
1.5 mM (M-1, Q1, M23L)rONC [U-15N; U-13C]
50mM phosphate buffer pH4.1, 90% H2O, 10% D2O
Nilges
structure solution
ARIA
1.2
Brunger
structure solution
CNS
1.1
Brunger
refinement
CNS
1.1
600
Bruker
DRX
MET
1
n
1
MET
1
A
GLN
2
n
2
GLN
2
A
ASP
3
n
3
ASP
3
A
TRP
4
n
4
TRP
4
A
LEU
5
n
5
LEU
5
A
THR
6
n
6
THR
6
A
PHE
7
n
7
PHE
7
A
GLN
8
n
8
GLN
8
A
LYS
9
n
9
LYS
9
A
LYS
10
n
10
LYS
10
A
HIS
11
n
11
HIS
11
A
ILE
12
n
12
ILE
12
A
THR
13
n
13
THR
13
A
ASN
14
n
14
ASN
14
A
THR
15
n
15
THR
15
A
ARG
16
n
16
ARG
16
A
ASP
17
n
17
ASP
17
A
VAL
18
n
18
VAL
18
A
ASP
19
n
19
ASP
19
A
CYS
20
n
20
CYS
20
A
ASP
21
n
21
ASP
21
A
ASN
22
n
22
ASN
22
A
ILE
23
n
23
ILE
23
A
LEU
24
n
24
LEU
24
A
SER
25
n
25
SER
25
A
THR
26
n
26
THR
26
A
ASN
27
n
27
ASN
27
A
LEU
28
n
28
LEU
28
A
PHE
29
n
29
PHE
29
A
HIS
30
n
30
HIS
30
A
CYS
31
n
31
CYS
31
A
LYS
32
n
32
LYS
32
A
ASP
33
n
33
ASP
33
A
LYS
34
n
34
LYS
34
A
ASN
35
n
35
ASN
35
A
THR
36
n
36
THR
36
A
PHE
37
n
37
PHE
37
A
ILE
38
n
38
ILE
38
A
TYR
39
n
39
TYR
39
A
SER
40
n
40
SER
40
A
ARG
41
n
41
ARG
41
A
PRO
42
n
42
PRO
42
A
GLU
43
n
43
GLU
43
A
PRO
44
n
44
PRO
44
A
VAL
45
n
45
VAL
45
A
LYS
46
n
46
LYS
46
A
ALA
47
n
47
ALA
47
A
ILE
48
n
48
ILE
48
A
CYS
49
n
49
CYS
49
A
LYS
50
n
50
LYS
50
A
GLY
51
n
51
GLY
51
A
ILE
52
n
52
ILE
52
A
ILE
53
n
53
ILE
53
A
ALA
54
n
54
ALA
54
A
SER
55
n
55
SER
55
A
LYS
56
n
56
LYS
56
A
ASN
57
n
57
ASN
57
A
VAL
58
n
58
VAL
58
A
LEU
59
n
59
LEU
59
A
THR
60
n
60
THR
60
A
THR
61
n
61
THR
61
A
SER
62
n
62
SER
62
A
GLU
63
n
63
GLU
63
A
PHE
64
n
64
PHE
64
A
TYR
65
n
65
TYR
65
A
LEU
66
n
66
LEU
66
A
SER
67
n
67
SER
67
A
ASP
68
n
68
ASP
68
A
CYS
69
n
69
CYS
69
A
ASN
70
n
70
ASN
70
A
VAL
71
n
71
VAL
71
A
THR
72
n
72
THR
72
A
SER
73
n
73
SER
73
A
ARG
74
n
74
ARG
74
A
PRO
75
n
75
PRO
75
A
CYS
76
n
76
CYS
76
A
LYS
77
n
77
LYS
77
A
TYR
78
n
78
TYR
78
A
LYS
79
n
79
LYS
79
A
LEU
80
n
80
LEU
80
A
LYS
81
n
81
LYS
81
A
LYS
82
n
82
LYS
82
A
SER
83
n
83
SER
83
A
THR
84
n
84
THR
84
A
ASN
85
n
85
ASN
85
A
LYS
86
n
86
LYS
86
A
PHE
87
n
87
PHE
87
A
CYS
88
n
88
CYS
88
A
VAL
89
n
89
VAL
89
A
THR
90
n
90
THR
90
A
CYS
91
n
91
CYS
91
A
GLU
92
n
92
GLU
92
A
ASN
93
n
93
ASN
93
A
GLN
94
n
94
GLN
94
A
ALA
95
n
95
ALA
95
A
PRO
96
n
96
PRO
96
A
VAL
97
n
97
VAL
97
A
HIS
98
n
98
HIS
98
A
PHE
99
n
99
PHE
99
A
VAL
100
n
100
VAL
100
A
GLY
101
n
101
GLY
101
A
VAL
102
n
102
VAL
102
A
GLY
103
n
103
GLY
103
A
SER
104
n
104
SER
104
A
CYS
105
n
105
CYS
105
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
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
THR
13
A
N
THR
13
A
O
ILE
38
A
O
ILE
38
A
N
TYR
39
A
N
TYR
39
A
O
TYR
65
A
O
TYR
65
A
N
ASP
68
A
N
ASP
68
A
O
LYS
81
A
O
LYS
81
A
N
LYS
56
A
N
LYS
56
A
O
CYS
91
A
O
CYS
91
A
N
THR
90
A
N
THR
90
A
O
HIS
98
A
O
HIS
98
1
A
A
OD2
HZ1
ASP
LYS
17
82
1.58
2
A
A
OE1
HZ2
GLU
LYS
63
86
1.59
4
A
A
OE2
HZ1
GLU
LYS
63
86
1.59
7
A
A
HA
HD2
ASP
TYR
21
78
1.34
8
A
A
OD1
HG1
ASP
THR
3
6
1.60
9
A
A
O
H
LYS
GLY
86
103
1.59
15
A
A
HA
HH
CYS
TYR
31
78
1.34
1
A
ASN
35
-161.56
115.79
1
A
SER
55
-51.81
105.02
1
A
THR
72
-89.24
-136.64
1
A
VAL
100
-95.54
-65.57
2
A
PHE
29
-136.01
-30.13
2
A
SER
40
-175.17
148.17
2
A
SER
55
-51.44
105.99
2
A
THR
72
-93.90
-145.59
3
A
ASN
27
-76.74
25.43
3
A
PHE
29
-133.98
-36.02
3
A
SER
55
-51.56
105.57
3
A
THR
72
-114.52
-82.32
3
A
SER
73
-94.71
-63.53
3
A
VAL
100
-80.13
-79.48
4
A
SER
55
-51.93
104.13
4
A
THR
72
-97.50
-99.17
4
A
VAL
100
-90.64
-72.39
5
A
PHE
29
-135.63
-33.91
5
A
CYS
31
38.78
62.72
5
A
THR
72
-87.26
-140.72
6
A
CYS
31
60.19
74.15
6
A
SER
55
-51.56
108.61
6
A
THR
72
-114.60
-105.48
6
A
PRO
96
-59.94
106.40
6
A
VAL
100
-79.81
-72.96
7
A
ASN
27
-78.50
25.25
7
A
ASN
35
-162.41
117.78
7
A
SER
55
-51.13
105.95
7
A
THR
72
-92.67
-98.31
8
A
CYS
31
40.40
79.42
8
A
SER
40
-176.59
-177.26
8
A
SER
55
-50.29
105.51
8
A
THR
72
-114.32
-113.05
9
A
GLN
2
64.57
112.76
9
A
SER
55
-51.30
106.96
9
A
THR
72
-88.89
-152.69
10
A
ASP
3
-170.05
-177.72
10
A
SER
40
-170.45
-177.50
10
A
SER
55
-50.85
102.43
10
A
THR
72
-90.69
-106.53
11
A
CYS
31
41.26
72.15
11
A
SER
55
-50.68
108.60
11
A
THR
72
-88.29
-144.54
12
A
SER
55
-51.39
109.60
12
A
THR
72
-97.67
-133.53
13
A
HIS
11
-140.77
-13.79
13
A
SER
40
-177.14
-172.36
13
A
SER
55
-51.89
106.19
13
A
THR
72
-95.58
-142.88
14
A
THR
72
-114.36
-108.63
14
A
VAL
100
-92.04
-64.82
15
A
PHE
29
-130.28
-35.16
15
A
CYS
31
48.17
79.74
15
A
LYS
32
-77.11
-168.99
15
A
SER
55
-48.82
101.07
15
A
THR
72
-87.30
-142.37
16
A
PHE
29
-133.47
-30.46
16
A
CYS
31
61.14
69.72
16
A
SER
40
-174.94
147.96
16
A
SER
55
-51.27
108.66
16
A
THR
72
-88.59
-135.00
17
A
SER
40
-177.56
-175.79
17
A
SER
55
-50.80
106.53
17
A
THR
72
-117.19
-102.07
17
A
VAL
100
-102.41
-70.22
18
A
GLN
2
68.44
156.90
18
A
PHE
29
-132.50
-46.95
18
A
SER
55
-53.35
104.36
18
A
THR
72
-92.58
-149.29
18
A
VAL
100
-85.19
-70.78
19
A
PHE
29
-140.88
-30.03
19
A
SER
55
-51.69
102.37
19
A
THR
72
-104.18
-144.88
19
A
VAL
100
-92.82
-72.94
20
A
PHE
29
-131.77
-41.90
20
A
CYS
31
39.51
73.64
20
A
ASN
35
-164.53
114.89
20
A
THR
72
-87.72
-146.95
20
A
VAL
100
-95.81
-69.15
minimized average
The Solution NMR Structure and Dynamics of a Recombinant Onconase with Altered N-terminal and Met23 residues
1
N
N
A
ASP
3
A
ASP
3
HELX_P
A
HIS
11
A
HIS
11
1
1
9
A
ASP
19
A
ASP
19
HELX_P
A
LEU
24
A
LEU
24
1
2
6
A
ARG
41
A
ARG
41
HELX_P
A
ALA
47
A
ALA
47
1
3
7
A
ILE
48
A
ILE
48
HELX_P
A
LYS
50
A
LYS
50
5
4
3
disulf
2.028
A
CYS
20
A
SG
CYS
20
1_555
A
CYS
69
A
SG
CYS
69
1_555
disulf
2.033
A
CYS
31
A
SG
CYS
31
1_555
A
CYS
76
A
SG
CYS
76
1_555
disulf
2.022
A
CYS
49
A
SG
CYS
49
1_555
A
CYS
91
A
SG
CYS
91
1_555
disulf
2.027
A
CYS
88
A
SG
CYS
88
1_555
A
CYS
105
A
SG
CYS
105
1_555
HYDROLASE
bowl-shaped folding of the two sheets, HYDROLASE
RN30_RANPI
UNP
1
1
P22069
QDWLTFQKKHITNTRDVDCDNIMSTNLFHCKDKNTFIYSRPEPVKAICKGIIASKNVLTTSEFYLSDCNVTSRPCKYKLK
KSTNKFCVTCENQAPVHFVGVGSC
1
104
1PU3
2
105
P22069
A
1
2
105
1
cloning artifact
MET
1
1PU3
A
P22069
UNP
1
1
MET
engineered mutation
LEU
24
1PU3
A
P22069
UNP
23
24
4
3
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
12
A
ILE
12
A
THR
13
A
THR
13
A
LYS
34
A
LYS
34
A
TYR
39
A
TYR
39
A
PHE
64
A
PHE
64
A
VAL
71
A
VAL
71
A
TYR
78
A
TYR
78
A
ASN
85
A
ASN
85
A
LYS
56
A
LYS
56
A
LEU
59
A
LEU
59
A
PHE
87
A
PHE
87
A
GLU
92
A
GLU
92
A
ALA
95
A
ALA
95
A
VAL
102
A
VAL
102