1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Wang, J.
Truckses, D.M.
Abildgaard, F.
Dzakula, Z.
Zolnai, Z.
Markley, J.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
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
NE
J.Biomol.NMR
JBNME9
0800
0925-2738
10
143
164
10.1023/A:1018350004729
9369015
Solution structures of staphylococcal nuclease from multidimensional, multinuclear NMR: nuclease-H124L and its ternary complex with Ca2+ and thymidine-3',5'-bisphosphate.
1997
10.2210/pdb1joo/pdb
pdb_00001joo
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
16818.340
staphylococcal nuclease
3.1.31.1
nuclease A
H124L
1
man
polymer
thermonuclease, tnase, micrococcal nuclease
no
no
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQLLRKSEAQAKKEKLNIWSEDNADSGQ
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQLLRKSEAQAKKEKLNIWSEDNADSGQ
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Staphylococcus
Escherichia
Escherichia coli
sample
1280
Staphylococcus aureus
469008
Escherichia coli BL21(DE3)
BL-21(DE3)
plasmid
pTSN2cc
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
2001-08-22
1
1
2008-04-27
1
2
2011-07-13
1
3
2021-10-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
AVERAGED STRUCTURE FOR STAPHYLOCOCCAL NUCLEASE-H124L IN TERNARY COMPLEX WITH CA2+ AND THYMIDINE-3',5'-BISPHOSPHATE
Ensemble structures for Staphylococcal nuclease-H124L in ternary complex with Ca2+ and thymidine-3',5'-bisphosphate
Ensemble structures for unligated Staphylococcal nuclease-H124L
RCSB
Y
RCSB
2001-07-30
REL
REL
1
E-COSY
HMQC-J
DQF-COSY
2D NOESY
2D NOESY
3D 1H-15N NOESY-HMQC
2D 1H-13C HMQC
HNCO
3D HNCA
and others
300 nM KCl
5.5
ambient
318
K
300 nM KCl
5.1
ambient
318
K
2176 constraints were used to calculate the structure
Distance, hydrogen bond and torsion angle constraints
minimized average structure
3.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; D2O
D2O
3.5-5 mM Nuclease-H124L U-95% 15N; 300 mM KCl; H2O
H2O
3.5-5 mM Nuclease-H124L; 300 mM KCl; D2O
D2O
3.5-5 mM Nuclease-H124L U-50% 2H; 300 mM KCl; H2O
H2O
3.5-5 mM Nuclease-H124L U-98% 13C; 300 mM KCl; H2O
H2O
3.5-5 mM Nuclease-H124L U-98% 13C U-99% 15N; 300 mM KCl; H2O
H2O
Biosym Technologies Inc
processing
Felix
Brunger
structure solution
X-PLOR
3.1
Biosym Technologies Inc
structure solution
Insight II
2.3
McDonald and Thornton
structure solution
HBPLUS
Brunger
refinement
X-PLOR
3.1
500
Bruker
AM
600
Bruker
AM
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
LYS
5
n
5
LYS
5
A
LYS
6
n
6
LYS
6
A
LEU
7
n
7
LEU
7
A
HIS
8
n
8
HIS
8
A
LYS
9
n
9
LYS
9
A
GLU
10
n
10
GLU
10
A
PRO
11
n
11
PRO
11
A
ALA
12
n
12
ALA
12
A
THR
13
n
13
THR
13
A
LEU
14
n
14
LEU
14
A
ILE
15
n
15
ILE
15
A
LYS
16
n
16
LYS
16
A
ALA
17
n
17
ALA
17
A
ILE
18
n
18
ILE
18
A
ASP
19
n
19
ASP
19
A
GLY
20
n
20
GLY
20
A
ASP
21
n
21
ASP
21
A
THR
22
n
22
THR
22
A
VAL
23
n
23
VAL
23
A
LYS
24
n
24
LYS
24
A
LEU
25
n
25
LEU
25
A
MET
26
n
26
MET
26
A
TYR
27
n
27
TYR
27
A
LYS
28
n
28
LYS
28
A
GLY
29
n
29
GLY
29
A
GLN
30
n
30
GLN
30
A
PRO
31
n
31
PRO
31
A
MET
32
n
32
MET
32
A
THR
33
n
33
THR
33
A
PHE
34
n
34
PHE
34
A
ARG
35
n
35
ARG
35
A
LEU
36
n
36
LEU
36
A
LEU
37
n
37
LEU
37
A
LEU
38
n
38
LEU
38
A
VAL
39
n
39
VAL
39
A
ASP
40
n
40
ASP
40
A
THR
41
n
41
THR
41
A
PRO
42
n
42
PRO
42
A
GLU
43
n
43
GLU
43
A
THR
44
n
44
THR
44
A
LYS
45
n
45
LYS
45
A
HIS
46
n
46
HIS
46
A
PRO
47
n
47
PRO
47
A
LYS
48
n
48
LYS
48
A
LYS
49
n
49
LYS
49
A
GLY
50
n
50
GLY
50
A
VAL
51
n
51
VAL
51
A
GLU
52
n
52
GLU
52
A
LYS
53
n
53
LYS
53
A
TYR
54
n
54
TYR
54
A
GLY
55
n
55
GLY
55
A
PRO
56
n
56
PRO
56
A
GLU
57
n
57
GLU
57
A
ALA
58
n
58
ALA
58
A
SER
59
n
59
SER
59
A
ALA
60
n
60
ALA
60
A
PHE
61
n
61
PHE
61
A
THR
62
n
62
THR
62
A
LYS
63
n
63
LYS
63
A
LYS
64
n
64
LYS
64
A
MET
65
n
65
MET
65
A
VAL
66
n
66
VAL
66
A
GLU
67
n
67
GLU
67
A
ASN
68
n
68
ASN
68
A
ALA
69
n
69
ALA
69
A
LYS
70
n
70
LYS
70
A
LYS
71
n
71
LYS
71
A
ILE
72
n
72
ILE
72
A
GLU
73
n
73
GLU
73
A
VAL
74
n
74
VAL
74
A
GLU
75
n
75
GLU
75
A
PHE
76
n
76
PHE
76
A
ASP
77
n
77
ASP
77
A
LYS
78
n
78
LYS
78
A
GLY
79
n
79
GLY
79
A
GLN
80
n
80
GLN
80
A
ARG
81
n
81
ARG
81
A
THR
82
n
82
THR
82
A
ASP
83
n
83
ASP
83
A
LYS
84
n
84
LYS
84
A
TYR
85
n
85
TYR
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
GLY
88
n
88
GLY
88
A
LEU
89
n
89
LEU
89
A
ALA
90
n
90
ALA
90
A
TYR
91
n
91
TYR
91
A
ILE
92
n
92
ILE
92
A
TYR
93
n
93
TYR
93
A
ALA
94
n
94
ALA
94
A
ASP
95
n
95
ASP
95
A
GLY
96
n
96
GLY
96
A
LYS
97
n
97
LYS
97
A
MET
98
n
98
MET
98
A
VAL
99
n
99
VAL
99
A
ASN
100
n
100
ASN
100
A
GLU
101
n
101
GLU
101
A
ALA
102
n
102
ALA
102
A
LEU
103
n
103
LEU
103
A
VAL
104
n
104
VAL
104
A
ARG
105
n
105
ARG
105
A
GLN
106
n
106
GLN
106
A
GLY
107
n
107
GLY
107
A
LEU
108
n
108
LEU
108
A
ALA
109
n
109
ALA
109
A
LYS
110
n
110
LYS
110
A
VAL
111
n
111
VAL
111
A
ALA
112
n
112
ALA
112
A
TYR
113
n
113
TYR
113
A
VAL
114
n
114
VAL
114
A
TYR
115
n
115
TYR
115
A
LYS
116
n
116
LYS
116
A
PRO
117
n
117
PRO
117
A
ASN
118
n
118
ASN
118
A
ASN
119
n
119
ASN
119
A
THR
120
n
120
THR
120
A
HIS
121
n
121
HIS
121
A
GLU
122
n
122
GLU
122
A
GLN
123
n
123
GLN
123
A
LEU
124
n
124
LEU
124
A
LEU
125
n
125
LEU
125
A
ARG
126
n
126
ARG
126
A
LYS
127
n
127
LYS
127
A
SER
128
n
128
SER
128
A
GLU
129
n
129
GLU
129
A
ALA
130
n
130
ALA
130
A
GLN
131
n
131
GLN
131
A
ALA
132
n
132
ALA
132
A
LYS
133
n
133
LYS
133
A
LYS
134
n
134
LYS
134
A
GLU
135
n
135
GLU
135
A
LYS
136
n
136
LYS
136
A
LEU
137
n
137
LEU
137
A
ASN
138
n
138
ASN
138
A
ILE
139
n
139
ILE
139
A
TRP
140
n
140
TRP
140
A
SER
141
n
141
SER
141
A
GLU
142
n
142
GLU
142
A
ASP
143
n
143
ASP
143
A
ASN
144
n
144
ASN
144
A
ALA
145
n
145
ALA
145
A
ASP
146
n
146
ASP
146
A
SER
147
n
147
SER
147
A
GLY
148
n
148
GLY
148
A
GLN
149
n
149
GLN
149
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
ILE
15
A
N
ILE
15
A
O
LYS
24
A
O
LYS
24
A
N
TYR
27
A
N
TYR
27
A
O
GLN
30
A
O
GLN
30
A
N
ARG
35
A
N
ARG
35
A
O
GLY
88
A
O
GLY
88
A
O
TYR
93
A
O
TYR
93
A
N
GLU
73
A
N
GLU
73
A
N
VAL
74
A
N
VAL
74
A
O
GLU
10
A
O
GLU
10
A
N
ILE
15
A
N
ILE
15
A
O
LYS
24
A
O
LYS
24
A
N
TYR
27
A
N
TYR
27
A
O
GLN
30
A
O
GLN
30
A
N
ARG
35
A
N
ARG
35
A
O
GLY
88
A
O
GLY
88
A
N
ALA
94
A
N
ALA
94
A
O
LYS
97
A
O
LYS
97
1
A
ARG
35
0.201
SIDE CHAIN
1
A
ARG
81
0.307
SIDE CHAIN
1
A
ARG
87
0.269
SIDE CHAIN
1
A
ARG
105
0.282
SIDE CHAIN
1
A
ARG
126
0.301
SIDE CHAIN
1
A
THR
2
52.38
177.63
1
A
LYS
5
73.15
153.87
1
A
LYS
16
-167.30
112.91
1
A
ILE
18
-121.47
-60.35
1
A
ASP
19
-118.98
-167.89
1
A
LYS
53
-88.10
-86.05
1
A
GLU
57
-127.43
-56.90
1
A
ALA
69
-48.86
96.48
1
A
GLN
80
-54.91
-176.58
1
A
ASP
83
-69.63
-157.00
1
A
ALA
90
-164.47
-169.45
1
A
MET
98
-63.93
98.02
1
A
ASN
118
-55.08
94.41
1
A
ASN
119
-160.13
36.26
1
A
THR
120
-75.50
-70.75
1
A
ASN
138
56.41
-104.80
1
A
ALA
145
-143.40
-52.09
1
A
SER
147
-111.81
68.92
minimized average
Averaged structure for unligated Staphylococcal nuclease-H124L
1
N
N
A
GLU
57
A
GLU
57
HELX_P
A
ALA
69
A
ALA
69
1
1
13
A
VAL
99
A
VAL
99
HELX_P
A
GLN
106
A
GLN
106
1
2
8
A
HIS
121
A
HIS
121
HELX_P
A
LYS
136
A
LYS
136
1
3
16
A
LEU
137
A
LEU
137
HELX_P
A
SER
141
A
SER
141
5
4
5
HYDROLASE
beta barrel, alpha helix, HYDROLASE
A
LYS
116
A
LYS
116
1
A
PRO
117
A
PRO
117
0.10
NUC_STAAU
UNP
1
83
P00644
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ
83
231
1JOO
1
149
P00644
A
1
1
149
1
HIS
engineered mutation
LEU
124
1JOO
A
P00644
UNP
206
124
6
5
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
THR
13
A
THR
13
A
ALA
17
A
ALA
17
A
THR
22
A
THR
22
A
TYR
27
A
TYR
27
A
GLN
30
A
GLN
30
A
LEU
36
A
LEU
36
A
GLY
88
A
GLY
88
A
ALA
94
A
ALA
94
A
ILE
72
A
ILE
72
A
PHE
76
A
PHE
76
A
GLU
10
A
GLU
10
A
PRO
11
A
PRO
11
A
THR
13
A
THR
13
A
ALA
17
A
ALA
17
A
THR
22
A
THR
22
A
TYR
27
A
TYR
27
A
GLN
30
A
GLN
30
A
LEU
36
A
LEU
36
A
GLY
88
A
GLY
88
A
ALA
94
A
ALA
94
A
LYS
97
A
LYS
97
A
MET
98
A
MET
98