0.010669
0.000000
0.004485
0.000000
0.026867
0.000000
0.000000
0.000000
0.019274
0.00000
0.00000
0.00000
Van Roey, P.
Silva, G.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
112.80
90.00
93.730
37.220
56.280
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
H2 O
18.015
WATER
non-polymer
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
286
1123
1136
10.1006/jmbi.1998.2519
10047486
Crystal structure of the thermostable archaeal intron-encoded endonuclease I-DmoI.
1999
10.2210/pdb1b24/pdb
pdb_00001b24
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
CCD
1997-09
BRANDEIS
MAD
M
x-ray
1
0.9300
1.0
0.9785
1.0
0.9789
1.0
X12C
NSLS
0.9300,0.9785,0.9789
SYNCHROTRON
NSLS BEAMLINE X12C
SELENOMETHIONYL PROTEIN
22181.473
Homing endonuclease I-DmoI
3.1.-.-
1
man
polymer
18.015
water
78
nat
water
no
yes
MHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPL(MSE)QFLIDELNVKSKIQIVKGDT
RYELRVSSKKLYYYFAN(MSE)LERIRLFN(MSE)REQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVR
NTIHLDDHRHGVYVLNISLRDRIKFVHTILSSHLNPLPPE
MHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYEL
RVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGV
YVLNISLRDRIKFVHTILSSHLNPLPPE
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Desulfurococcus
Escherichia
sample
1
SELENOMETHIONINE AUXOTROPH
188
2275
Desulfurococcus mobilis
562
Escherichia coli
DL41(DE3)
Biological sequence
1
2.01
33.3
MAD DATA TREATED AS A SPECIAL CASE OF MIR
VAPOR DIFFUSION, HANGING DROP
8.5
HANGING DROP VAPOR-DIFFUSION METHOD: 4UL I-DMOI PROTEIN 1UL 20MM N-OCTYL-B-
GLUCOPYRANOSIDE 4UL PRECIPITATING BUFFER: 30% PEG 3350 200MM SODIUM ACETATE
100MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, HANGING DROP
4UL I-DMOI PROTEIN
1
1UL 20MM N-OCTYL-B-GLUCOPYRANOSIDE
2
4UL PRECIPITATING BUFFER
2
30% PEG 3350
2
200MM SODIUM ACETATE
2
100MM TRIS-HCL PH 8.5
2
database_2
entity
entity_src_gen
pdbx_struct_mod_residue
struct_conn
struct_ref
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Source and taxonomy
Structure summary
1
0
1999-03-24
1
1
2008-04-26
1
2
2011-07-13
1
3
2022-12-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_entity.pdbx_description
_entity.pdbx_ec
_entity_src_gen.pdbx_beg_seq_num
_entity_src_gen.pdbx_end_seq_num
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
_entity_src_gen.pdbx_seq_type
_pdbx_struct_mod_residue.details
_struct_conn.pdbx_leaving_atom_flag
_struct_ref.pdbx_align_begin
_struct_ref.pdbx_seq_one_letter_code
BNL
Y
RCSB
1998-12-03
REL
REL
HOH
water
HOH
1
2
HOH
HOH
189
A
HOH
2
2
HOH
HOH
190
A
HOH
6
2
HOH
HOH
191
A
HOH
9
2
HOH
HOH
192
A
HOH
12
2
HOH
HOH
193
A
HOH
13
2
HOH
HOH
194
A
HOH
14
2
HOH
HOH
195
A
HOH
15
2
HOH
HOH
196
A
HOH
16
2
HOH
HOH
197
A
HOH
17
2
HOH
HOH
198
A
HOH
20
2
HOH
HOH
199
A
HOH
22
2
HOH
HOH
200
A
HOH
23
2
HOH
HOH
201
A
HOH
24
2
HOH
HOH
202
A
HOH
25
2
HOH
HOH
203
A
HOH
26
2
HOH
HOH
204
A
HOH
28
2
HOH
HOH
205
A
HOH
30
2
HOH
HOH
206
A
HOH
31
2
HOH
HOH
207
A
HOH
33
2
HOH
HOH
208
A
HOH
36
2
HOH
HOH
209
A
HOH
37
2
HOH
HOH
210
A
HOH
38
2
HOH
HOH
211
A
HOH
40
2
HOH
HOH
212
A
HOH
43
2
HOH
HOH
213
A
HOH
45
2
HOH
HOH
214
A
HOH
47
2
HOH
HOH
215
A
HOH
48
2
HOH
HOH
216
A
HOH
49
2
HOH
HOH
217
A
HOH
50
2
HOH
HOH
218
A
HOH
51
2
HOH
HOH
219
A
HOH
52
2
HOH
HOH
220
A
HOH
54
2
HOH
HOH
221
A
HOH
55
2
HOH
HOH
222
A
HOH
56
2
HOH
HOH
223
A
HOH
58
2
HOH
HOH
224
A
HOH
59
2
HOH
HOH
225
A
HOH
60
2
HOH
HOH
226
A
HOH
61
2
HOH
HOH
227
A
HOH
62
2
HOH
HOH
228
A
HOH
63
2
HOH
HOH
229
A
HOH
65
2
HOH
HOH
230
A
HOH
66
2
HOH
HOH
231
A
HOH
67
2
HOH
HOH
232
A
HOH
68
2
HOH
HOH
233
A
HOH
71
2
HOH
HOH
234
A
HOH
72
2
HOH
HOH
235
A
HOH
73
2
HOH
HOH
236
A
HOH
74
2
HOH
HOH
237
A
HOH
75
2
HOH
HOH
238
A
HOH
76
2
HOH
HOH
239
A
HOH
80
2
HOH
HOH
240
A
HOH
81
2
HOH
HOH
241
A
HOH
82
2
HOH
HOH
242
A
HOH
83
2
HOH
HOH
243
A
HOH
87
2
HOH
HOH
244
A
HOH
91
2
HOH
HOH
245
A
HOH
92
2
HOH
HOH
246
A
HOH
93
2
HOH
HOH
247
A
HOH
94
2
HOH
HOH
248
A
HOH
95
2
HOH
HOH
249
A
HOH
96
2
HOH
HOH
250
A
HOH
100
2
HOH
HOH
251
A
HOH
101
2
HOH
HOH
252
A
HOH
102
2
HOH
HOH
253
A
HOH
103
2
HOH
HOH
254
A
HOH
104
2
HOH
HOH
255
A
HOH
106
2
HOH
HOH
256
A
HOH
107
2
HOH
HOH
257
A
HOH
108
2
HOH
HOH
258
A
HOH
109
2
HOH
HOH
259
A
HOH
111
2
HOH
HOH
260
A
HOH
112
2
HOH
HOH
261
A
HOH
113
2
HOH
HOH
262
A
HOH
116
2
HOH
HOH
263
A
HOH
117
2
HOH
HOH
264
A
HOH
118
2
HOH
HOH
265
A
HOH
119
2
HOH
HOH
266
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
VAL
7
n
7
VAL
7
A
SER
8
n
8
SER
8
A
GLY
9
n
9
GLY
9
A
ILE
10
n
10
ILE
10
A
SER
11
n
11
SER
11
A
ALA
12
n
12
ALA
12
A
TYR
13
n
13
TYR
13
A
LEU
14
n
14
LEU
14
A
LEU
15
n
15
LEU
15
A
GLY
16
n
16
GLY
16
A
LEU
17
n
17
LEU
17
A
ILE
18
n
18
ILE
18
A
ILE
19
n
19
ILE
19
A
GLY
20
n
20
GLY
20
A
ASP
21
n
21
ASP
21
A
GLY
22
n
22
GLY
22
A
GLY
23
n
23
GLY
23
A
LEU
24
n
24
LEU
24
A
TYR
25
n
25
TYR
25
A
LYS
26
n
26
LYS
26
A
LEU
27
n
27
LEU
27
A
LYS
28
n
28
LYS
28
A
TYR
29
n
29
TYR
29
A
LYS
30
n
30
LYS
30
A
GLY
31
n
31
GLY
31
A
ASN
32
n
32
ASN
32
A
ARG
33
n
33
ARG
33
A
SER
34
n
34
SER
34
A
GLU
35
n
35
GLU
35
A
TYR
36
n
36
TYR
36
A
ARG
37
n
37
ARG
37
A
VAL
38
n
38
VAL
38
A
VAL
39
n
39
VAL
39
A
ILE
40
n
40
ILE
40
A
THR
41
n
41
THR
41
A
GLN
42
n
42
GLN
42
A
LYS
43
n
43
LYS
43
A
SER
44
n
44
SER
44
A
GLU
45
n
45
GLU
45
A
ASN
46
n
46
ASN
46
A
LEU
47
n
47
LEU
47
A
ILE
48
n
48
ILE
48
A
LYS
49
n
49
LYS
49
A
GLN
50
n
50
GLN
50
A
HIS
51
n
51
HIS
51
A
ILE
52
n
52
ILE
52
A
ALA
53
n
53
ALA
53
A
PRO
54
n
54
PRO
54
A
LEU
55
n
55
LEU
55
A
MSE
56
n
56
MSE
56
A
GLN
57
n
57
GLN
57
A
PHE
58
n
58
PHE
58
A
LEU
59
n
59
LEU
59
A
ILE
60
n
60
ILE
60
A
ASP
61
n
61
ASP
61
A
GLU
62
n
62
GLU
62
A
LEU
63
n
63
LEU
63
A
ASN
64
n
64
ASN
64
A
VAL
65
n
65
VAL
65
A
LYS
66
n
66
LYS
66
A
SER
67
n
67
SER
67
A
LYS
68
n
68
LYS
68
A
ILE
69
n
69
ILE
69
A
GLN
70
n
70
GLN
70
A
ILE
71
n
71
ILE
71
A
VAL
72
n
72
VAL
72
A
LYS
73
n
73
LYS
73
A
GLY
74
n
74
GLY
74
A
ASP
75
n
75
ASP
75
A
THR
76
n
76
THR
76
A
ARG
77
n
77
ARG
77
A
TYR
78
n
78
TYR
78
A
GLU
79
n
79
GLU
79
A
LEU
80
n
80
LEU
80
A
ARG
81
n
81
ARG
81
A
VAL
82
n
82
VAL
82
A
SER
83
n
83
SER
83
A
SER
84
n
84
SER
84
A
LYS
85
n
85
LYS
85
A
LYS
86
n
86
LYS
86
A
LEU
87
n
87
LEU
87
A
TYR
88
n
88
TYR
88
A
TYR
89
n
89
TYR
89
A
TYR
90
n
90
TYR
90
A
PHE
91
n
91
PHE
91
A
ALA
92
n
92
ALA
92
A
ASN
93
n
93
ASN
93
A
MSE
94
n
94
MSE
94
A
LEU
95
n
95
LEU
95
A
GLU
96
n
96
GLU
96
A
ARG
97
n
97
ARG
97
A
ILE
98
n
98
ILE
98
A
ARG
99
n
99
ARG
99
A
LEU
100
n
100
LEU
100
A
PHE
101
n
101
PHE
101
A
ASN
102
n
102
ASN
102
A
MSE
103
n
103
MSE
103
A
ARG
104
n
104
ARG
104
A
GLU
105
n
105
GLU
105
A
GLN
106
n
106
GLN
106
A
ILE
107
n
107
ILE
107
A
ALA
108
n
108
ALA
108
A
PHE
109
n
109
PHE
109
A
ILE
110
n
110
ILE
110
A
LYS
111
n
111
LYS
111
A
GLY
112
n
112
GLY
112
A
LEU
113
n
113
LEU
113
A
TYR
114
n
114
TYR
114
A
VAL
115
n
115
VAL
115
A
ALA
116
n
116
ALA
116
A
GLU
117
n
117
GLU
117
A
GLY
118
n
118
GLY
118
A
ASP
119
n
119
ASP
119
A
LYS
120
n
120
LYS
120
A
THR
121
n
121
THR
121
A
LEU
122
n
122
LEU
122
A
LYS
123
n
123
LYS
123
A
ARG
124
n
124
ARG
124
A
LEU
125
n
125
LEU
125
A
ARG
126
n
126
ARG
126
A
ILE
127
n
127
ILE
127
A
TRP
128
n
128
TRP
128
A
ASN
129
n
129
ASN
129
A
LYS
130
n
130
LYS
130
A
ASN
131
n
131
ASN
131
A
LYS
132
n
132
LYS
132
A
ALA
133
n
133
ALA
133
A
LEU
134
n
134
LEU
134
A
LEU
135
n
135
LEU
135
A
GLU
136
n
136
GLU
136
A
ILE
137
n
137
ILE
137
A
VAL
138
n
138
VAL
138
A
SER
139
n
139
SER
139
A
ARG
140
n
140
ARG
140
A
TRP
141
n
141
TRP
141
A
LEU
142
n
142
LEU
142
A
ASN
143
n
143
ASN
143
A
ASN
144
n
144
ASN
144
A
LEU
145
n
145
LEU
145
A
GLY
146
n
146
GLY
146
A
VAL
147
n
147
VAL
147
A
ARG
148
n
148
ARG
148
A
ASN
149
n
149
ASN
149
A
THR
150
n
150
THR
150
A
ILE
151
n
151
ILE
151
A
HIS
152
n
152
HIS
152
A
LEU
153
n
153
LEU
153
A
ASP
154
n
154
ASP
154
A
ASP
155
n
155
ASP
155
A
HIS
156
n
156
HIS
156
A
ARG
157
n
157
ARG
157
A
HIS
158
n
158
HIS
158
A
GLY
159
n
159
GLY
159
A
VAL
160
n
160
VAL
160
A
TYR
161
n
161
TYR
161
A
VAL
162
n
162
VAL
162
A
LEU
163
n
163
LEU
163
A
ASN
164
n
164
ASN
164
A
ILE
165
n
165
ILE
165
A
SER
166
n
166
SER
166
A
LEU
167
n
167
LEU
167
A
ARG
168
n
168
ARG
168
A
ASP
169
n
169
ASP
169
A
ARG
170
n
170
ARG
170
A
ILE
171
n
171
ILE
171
A
LYS
172
n
172
LYS
172
A
PHE
173
n
173
PHE
173
A
VAL
174
n
174
VAL
174
A
HIS
175
n
175
HIS
175
A
THR
176
n
176
THR
176
A
ILE
177
n
177
ILE
177
A
LEU
178
n
178
LEU
178
A
SER
179
n
179
SER
179
A
n
180
180
A
n
181
181
A
n
182
182
A
n
183
183
A
n
184
184
A
n
185
185
A
n
186
186
A
n
187
187
A
n
188
188
A
author_defined_assembly
1
monomeric
A
MSE
56
modified residue
A
MSE
56
MET
A
MSE
94
modified residue
A
MSE
94
MET
A
MSE
103
modified residue
A
MSE
103
MET
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
O
GLY
23
A
O
GLY
23
A
N
VAL
39
A
N
VAL
39
A
O
VAL
38
A
O
VAL
38
A
N
VAL
82
A
N
VAL
82
A
O
GLU
79
A
O
GLU
79
A
N
VAL
72
A
N
VAL
72
A
O
ILE
127
A
O
ILE
127
A
N
LEU
163
A
N
LEU
163
A
O
VAL
160
A
O
VAL
160
A
N
ASP
155
A
N
ASP
155
1
A
CA
SER
179
A
CA
SER
179
1
Y
1
A
C
SER
179
A
C
SER
179
1
Y
1
A
O
SER
179
A
O
SER
179
1
Y
1
A
CB
SER
179
A
CB
SER
179
1
Y
1
A
OG
SER
179
A
OG
SER
179
1
Y
1
A
MET
1
A
MET
1
1
Y
1
A
HIS
2
A
HIS
2
1
Y
1
A
ASN
3
A
ASN
3
1
Y
1
A
ASN
4
A
ASN
4
1
Y
1
A
GLU
5
A
GLU
5
1
Y
1
A
ASN
6
A
ASN
6
1
Y
1
A
SER
180
A
SER
180
1
Y
1
A
HIS
181
A
HIS
181
1
Y
1
A
LEU
182
A
LEU
182
1
Y
1
A
ASN
183
A
ASN
183
1
Y
1
A
PRO
184
A
PRO
184
1
Y
1
A
LEU
185
A
LEU
185
1
Y
1
A
PRO
186
A
PRO
186
1
Y
1
A
PRO
187
A
PRO
187
1
Y
1
A
GLU
188
A
GLU
188
1
Y
1
A
A
O
O
HOH
HOH
210
255
1.86
1
A
A
O
O
HOH
HOH
229
234
1.88
1
A
A
O
O
HOH
HOH
237
257
1.95
1
A
A
O
O
HOH
HOH
203
230
2.03
1
A
A
O
O
HOH
HOH
230
255
2.19
1
A
ASP
21
-158.15
88.02
1
A
TYR
29
-91.46
-77.37
1
A
HIS
51
-130.99
-62.66
1
A
THR
76
84.47
-38.74
1
A
ARG
97
-96.58
42.29
PROTEIN_REP.PARAM
TOPHCSDX.PRO
PARAM19.SOL
TOPH19.SOL
TOPH19.PEP
PARHCSDX.PRO
0.3240000
0.2180000
2.2
10.0
887
8878
10.0
98.7
RANDOM
1
THROUGHOUT
0.0
MAD
2.2
10.0
78
1505
0
0
1427
0.007
1.285
26.23
0.609
0.3613000
0.2996000
2.30
80
737
8
10.0
98.7
2.2
20.0
1B24
8884
0.0
0.059
1
32.3
11.1
98.5
2.20
2.28
24.7
0.070
6
97.4
phasing
PHASES
refinement
X-PLOR
3.851
data reduction
DENZO
data scaling
SCALEPACK
I-DMOI, INTRON-ENCODED ENDONUCLEASE
1
N
N
2
N
N
A
SER
8
A
SER
8
HELX_P
A
GLY
20
A
GLY
20
1
1
13
A
GLU
45
A
GLU
45
HELX_P
A
GLN
50
A
GLN
50
1
2
6
A
PRO
54
A
PRO
54
HELX_P
A
GLU
62
A
GLU
62
5
3
9
A
LYS
85
A
LYS
85
HELX_P
A
ALA
92
A
ALA
92
1
4
8
A
ILE
98
A
ILE
98
HELX_P
A
LEU
100
A
LEU
100
5
5
3
A
GLU
105
A
GLU
105
HELX_P
A
GLU
117
A
GLU
117
1
6
13
A
LYS
132
A
LYS
132
HELX_P
A
LEU
145
A
LEU
145
1
7
14
A
LEU
167
A
LEU
167
HELX_P
A
THR
176
A
THR
176
5
8
10
covale
1.330
both
A
LEU
55
A
C
LEU
55
1_555
A
MSE
56
A
N
MSE
56
1_555
covale
1.330
both
A
MSE
56
A
C
MSE
56
1_555
A
GLN
57
A
N
GLN
57
1_555
covale
1.335
both
A
ASN
93
A
C
ASN
93
1_555
A
MSE
94
A
N
MSE
94
1_555
covale
1.327
both
A
MSE
94
A
C
MSE
94
1_555
A
LEU
95
A
N
LEU
95
1_555
covale
1.323
both
A
ASN
102
A
C
ASN
102
1_555
A
MSE
103
A
N
MSE
103
1_555
covale
1.328
both
A
MSE
103
A
C
MSE
103
1_555
A
ARG
104
A
N
ARG
104
1_555
INTRON-ENCODED
INTRON-ENCODED, ENDONUCLEASE, HOMING, THERMOSTABLE
DMO1_DESMO
UNP
1
1
P21505
MHNNENVSGISAYLLGLIIGDGGLYKLKYKGNRSEYRVVITQKSENLIKQHIAPLMQFLIDELNVKSKIQIVKGDTRYEL
RVSSKKLYYYFANMLERIRLFNMREQIAFIKGLYVAEGDKTLKRLRIWNKNKALLEIVSRWLNNLGVRNTIHLDDHRHGV
YVLNISLRDRIKFVHTILSSHLNPLPPE
1
188
1B24
1
188
P21505
A
1
1
188
4
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLY
22
A
GLY
22
A
LYS
28
A
LYS
28
A
SER
34
A
SER
34
A
GLN
42
A
GLN
42
A
TYR
78
A
TYR
78
A
SER
83
A
SER
83
A
GLN
70
A
GLN
70
A
LYS
73
A
LYS
73
A
ARG
126
A
ARG
126
A
ASN
129
A
ASN
129
A
VAL
160
A
VAL
160
A
ILE
165
A
ILE
165
A
ASN
149
A
ASN
149
A
ASP
155
A
ASP
155
5
C 1 2 1