0.017191
0.009925
0.000000
0.000000
0.019850
0.000000
0.000000
0.000000
0.014229
0.00000
0.00000
0.00000
Ding, Y.
Chen, X.
Ferrandon, S.
Xu, M.
Rao, Z.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90
90
120
58.17
58.17
70.28
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
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
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
278
39133
39142
10.1074/jbc.M306197200
12878593
Crystal structure of mini-intein reveals a conserved catalytic module involved in side chain cyclization of asparagine during protein splicing
2003
10.2210/pdb1mi8/pdb
pdb_00001mi8
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
1
IMAGE PLATE
2002-05-08
MARRESEARCH
osmic mirror
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
TETHERED DIMER LINKED BY LESSSLQLSPEIEKLSQ
17600.168
DnaB intein
3.6.1.-
1
man
polymer
18.015
water
50
nat
water
Replicative DNA helicase
no
no
SGAISGDSLISLASTGKRVSIKDLLDEKDFEIWAINEQTMKLESAKVSRVFMTGKKLVYILKTRLGRTIKATANHRFLTI
DGWKRLDELSLKEHIALPRKLESSSLQLSPEIEKLSQSDISWDSIVSITETGVEEVFDLTVPGPHNFVANDIIVHASI
SGAISGDSLISLASTGKRVSIKDLLDEKDFEIWAINEQTMKLESAKVSRVFMTGKKLVYILKTRLGRTIKATANHRFLTI
DGWKRLDELSLKEHIALPRKLESSSLQLSPEIEKLSQSDISWDSIVSITETGVEEVFDLTVPGPHNFVANDIIVHASI
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
Synechocystis
PCC 6803
Escherichia
sample
1
100
1148
Synechocystis sp.
562
Escherichia coli
PLASMID
pTWIN
Synechocystis
PCC 6803
Escherichia
sample
118
158
1148
Synechocystis sp.
562
Escherichia coli
PLASMID
pTWIN
1
1.95
36.92
VAPOR DIFFUSION, HANGING DROP
7.8
PEG4000, Tris-HCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
entity_src_gen
software
database_2
struct_ref_seq_dif
repository
Initial release
Version format compliance
Source and taxonomy
Version format compliance
Refinement description
Source and taxonomy
Database references
1
0
2003-08-19
1
1
2008-04-28
1
2
2011-07-13
1
3
2017-08-23
1
4
2021-11-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
RCSB
Y
PDBJ
2002-08-22
REL
REL
HOH
water
TIP
1
2
HOH
HOH
157
A
TIP
2
2
HOH
HOH
158
A
TIP
3
2
HOH
HOH
159
A
TIP
4
2
HOH
HOH
160
A
TIP
5
2
HOH
HOH
161
A
TIP
6
2
HOH
HOH
162
A
TIP
7
2
HOH
HOH
163
A
TIP
8
2
HOH
HOH
164
A
TIP
9
2
HOH
HOH
165
A
TIP
10
2
HOH
HOH
166
A
TIP
11
2
HOH
HOH
167
A
TIP
12
2
HOH
HOH
168
A
TIP
13
2
HOH
HOH
169
A
TIP
14
2
HOH
HOH
170
A
TIP
15
2
HOH
HOH
171
A
TIP
16
2
HOH
HOH
172
A
TIP
17
2
HOH
HOH
173
A
TIP
18
2
HOH
HOH
174
A
TIP
19
2
HOH
HOH
175
A
TIP
20
2
HOH
HOH
176
A
TIP
21
2
HOH
HOH
177
A
TIP
22
2
HOH
HOH
178
A
TIP
23
2
HOH
HOH
179
A
TIP
24
2
HOH
HOH
180
A
TIP
26
2
HOH
HOH
181
A
TIP
27
2
HOH
HOH
182
A
TIP
28
2
HOH
HOH
183
A
TIP
29
2
HOH
HOH
184
A
TIP
30
2
HOH
HOH
185
A
TIP
31
2
HOH
HOH
186
A
TIP
32
2
HOH
HOH
187
A
TIP
33
2
HOH
HOH
188
A
TIP
34
2
HOH
HOH
189
A
TIP
35
2
HOH
HOH
190
A
TIP
36
2
HOH
HOH
191
A
TIP
37
2
HOH
HOH
192
A
TIP
38
2
HOH
HOH
193
A
TIP
39
2
HOH
HOH
194
A
TIP
41
2
HOH
HOH
195
A
TIP
42
2
HOH
HOH
196
A
TIP
43
2
HOH
HOH
197
A
TIP
44
2
HOH
HOH
198
A
TIP
45
2
HOH
HOH
199
A
TIP
46
2
HOH
HOH
200
A
TIP
47
2
HOH
HOH
201
A
TIP
48
2
HOH
HOH
202
A
TIP
49
2
HOH
HOH
203
A
TIP
50
2
HOH
HOH
204
A
TIP
51
2
HOH
HOH
205
A
TIP
52
2
HOH
HOH
206
A
SER
-2
n
1
SER
-2
A
GLY
-1
n
2
GLY
-1
A
ALA
1
n
3
ALA
1
A
ILE
2
n
4
ILE
2
A
SER
3
n
5
SER
3
A
GLY
4
n
6
GLY
4
A
ASP
5
n
7
ASP
5
A
SER
6
n
8
SER
6
A
LEU
7
n
9
LEU
7
A
ILE
8
n
10
ILE
8
A
SER
9
n
11
SER
9
A
LEU
10
n
12
LEU
10
A
ALA
11
n
13
ALA
11
A
SER
12
n
14
SER
12
A
THR
13
n
15
THR
13
A
GLY
14
n
16
GLY
14
A
LYS
15
n
17
LYS
15
A
ARG
16
n
18
ARG
16
A
VAL
17
n
19
VAL
17
A
SER
18
n
20
SER
18
A
ILE
19
n
21
ILE
19
A
LYS
20
n
22
LYS
20
A
ASP
21
n
23
ASP
21
A
LEU
22
n
24
LEU
22
A
LEU
23
n
25
LEU
23
A
ASP
24
n
26
ASP
24
A
GLU
25
n
27
GLU
25
A
LYS
26
n
28
LYS
26
A
ASP
27
n
29
ASP
27
A
PHE
28
n
30
PHE
28
A
GLU
29
n
31
GLU
29
A
ILE
30
n
32
ILE
30
A
TRP
31
n
33
TRP
31
A
ALA
32
n
34
ALA
32
A
ILE
33
n
35
ILE
33
A
ASN
34
n
36
ASN
34
A
GLU
35
n
37
GLU
35
A
GLN
36
n
38
GLN
36
A
THR
37
n
39
THR
37
A
MET
38
n
40
MET
38
A
LYS
39
n
41
LYS
39
A
LEU
40
n
42
LEU
40
A
GLU
41
n
43
GLU
41
A
SER
42
n
44
SER
42
A
ALA
43
n
45
ALA
43
A
LYS
44
n
46
LYS
44
A
VAL
45
n
47
VAL
45
A
SER
46
n
48
SER
46
A
ARG
47
n
49
ARG
47
A
VAL
48
n
50
VAL
48
A
PHE
49
n
51
PHE
49
A
MET
50
n
52
MET
50
A
THR
51
n
53
THR
51
A
GLY
52
n
54
GLY
52
A
LYS
53
n
55
LYS
53
A
LYS
54
n
56
LYS
54
A
LEU
55
n
57
LEU
55
A
VAL
56
n
58
VAL
56
A
TYR
57
n
59
TYR
57
A
ILE
58
n
60
ILE
58
A
LEU
59
n
61
LEU
59
A
LYS
60
n
62
LYS
60
A
THR
61
n
63
THR
61
A
ARG
62
n
64
ARG
62
A
LEU
63
n
65
LEU
63
A
GLY
64
n
66
GLY
64
A
ARG
65
n
67
ARG
65
A
THR
66
n
68
THR
66
A
ILE
67
n
69
ILE
67
A
LYS
68
n
70
LYS
68
A
ALA
69
n
71
ALA
69
A
THR
70
n
72
THR
70
A
ALA
71
n
73
ALA
71
A
ASN
72
n
74
ASN
72
A
HIS
73
n
75
HIS
73
A
ARG
74
n
76
ARG
74
A
PHE
75
n
77
PHE
75
A
LEU
76
n
78
LEU
76
A
THR
77
n
79
THR
77
A
ILE
78
n
80
ILE
78
A
ASP
79
n
81
ASP
79
A
GLY
80
n
82
GLY
80
A
TRP
81
n
83
TRP
81
A
LYS
82
n
84
LYS
82
A
ARG
83
n
85
ARG
83
A
LEU
84
n
86
LEU
84
A
ASP
85
n
87
ASP
85
A
GLU
86
n
88
GLU
86
A
LEU
87
n
89
LEU
87
A
SER
88
n
90
SER
88
A
LEU
89
n
91
LEU
89
A
LYS
90
n
92
LYS
90
A
GLU
91
n
93
GLU
91
A
HIS
92
n
94
HIS
92
A
ILE
93
n
95
ILE
93
A
ALA
94
n
96
ALA
94
A
LEU
95
n
97
LEU
95
A
PRO
96
n
98
PRO
96
A
ARG
97
n
99
ARG
97
A
LYS
98
n
100
LYS
98
A
n
101
99
A
n
102
100
A
n
103
101
A
n
104
102
A
n
105
103
A
n
106
104
A
n
107
105
A
n
108
106
A
n
109
107
A
n
110
108
A
n
111
109
A
n
112
110
A
n
113
111
A
n
114
112
A
n
115
113
A
n
116
114
A
n
117
115
A
SER
116
n
118
SER
116
A
ASP
117
n
119
ASP
117
A
ILE
118
n
120
ILE
118
A
SER
119
n
121
SER
119
A
TRP
120
n
122
TRP
120
A
ASP
121
n
123
ASP
121
A
SER
122
n
124
SER
122
A
ILE
123
n
125
ILE
123
A
VAL
124
n
126
VAL
124
A
SER
125
n
127
SER
125
A
ILE
126
n
128
ILE
126
A
THR
127
n
129
THR
127
A
GLU
128
n
130
GLU
128
A
THR
129
n
131
THR
129
A
GLY
130
n
132
GLY
130
A
VAL
131
n
133
VAL
131
A
GLU
132
n
134
GLU
132
A
GLU
133
n
135
GLU
133
A
VAL
134
n
136
VAL
134
A
PHE
135
n
137
PHE
135
A
ASP
136
n
138
ASP
136
A
LEU
137
n
139
LEU
137
A
THR
138
n
140
THR
138
A
VAL
139
n
141
VAL
139
A
PRO
140
n
142
PRO
140
A
GLY
141
n
143
GLY
141
A
PRO
142
n
144
PRO
142
A
HIS
143
n
145
HIS
143
A
ASN
144
n
146
ASN
144
A
PHE
145
n
147
PHE
145
A
VAL
146
n
148
VAL
146
A
ALA
147
n
149
ALA
147
A
ASN
148
n
150
ASN
148
A
ASP
149
n
151
ASP
149
A
ILE
150
n
152
ILE
150
A
ILE
151
n
153
ILE
151
A
VAL
152
n
154
VAL
152
A
HIS
153
n
155
HIS
153
A
ALA
154
n
156
ALA
154
A
SER
155
n
157
SER
155
A
ILE
156
n
158
ILE
156
A
author_defined_assembly
2
dimeric
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
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
5_555
x-y,-y,-z+1/3
crystal symmetry operation
0.0000000000
0.0000000000
23.4266666667
A
N
ILE
2
A
N
ILE
4
A
O
PHE
135
A
O
PHE
137
A
O
GLU
132
A
O
GLU
134
A
N
LYS
54
A
N
LYS
56
A
N
LEU
59
A
N
LEU
61
A
O
ILE
67
A
O
ILE
69
A
N
ILE
2
A
N
ILE
4
A
O
PHE
135
A
O
PHE
137
A
O
ASP
121
A
O
ASP
123
A
N
ILE
93
A
N
ILE
95
A
N
ILE
8
A
N
ILE
10
A
O
VAL
17
A
O
VAL
19
A
N
ILE
30
A
N
ILE
32
A
O
ALA
43
A
O
ALA
45
A
N
PHE
75
A
N
PHE
77
A
O
LYS
82
A
O
LYS
84
A
N
PHE
145
A
N
PHE
147
A
O
VAL
152
A
O
VAL
154
1
A
LEU
99
A
LEU
101
1
Y
1
A
GLU
100
A
GLU
102
1
Y
1
A
SER
101
A
SER
103
1
Y
1
A
SER
102
A
SER
104
1
Y
1
A
SER
103
A
SER
105
1
Y
1
A
LEU
104
A
LEU
106
1
Y
1
A
GLN
105
A
GLN
107
1
Y
1
A
LEU
106
A
LEU
108
1
Y
1
A
SER
107
A
SER
109
1
Y
1
A
PRO
108
A
PRO
110
1
Y
1
A
GLU
109
A
GLU
111
1
Y
1
A
ILE
110
A
ILE
112
1
Y
1
A
GLU
111
A
GLU
113
1
Y
1
A
LYS
112
A
LYS
114
1
Y
1
A
LEU
113
A
LEU
115
1
Y
1
A
SER
114
A
SER
116
1
Y
1
A
GLN
115
A
GLN
117
1
Y
1
-3.24
0.50
120.30
117.06
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
65
65
65
N
1
A
ALA
1
173.50
150.90
1
A
ASP
24
-100.20
52.42
1
A
SER
155
-33.73
141.17
0.263
0.21
0.237
0.226
2.0
20.0
919
9677
8794
RANDOM
1
2
MOLECULAR REPLACEMENT
Engh & Huber
2.0
20.0
50
1157
0
0
1107
0.018
2.04
2.0
50
1MI8
9307
1
1
1
99.9
2.0
2.07
1
75.5
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
CNS
1.0
2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803
1
N
N
2
N
N
The biological assembly is a dimer generated from the monomer in the asymmetric unit
A
LYS
20
A
LYS
22
HELX_P
A
LEU
23
A
LEU
25
5
1
4
A
ASP
85
A
ASP
87
HELX_P
A
LEU
87
A
LEU
89
5
2
3
HYDROLASE
all beta-strands, Hydrolase
DNAB_SYNY3
UNP
1
Q55418
379
478
1MI8
-2
98
Q55418
A
1
1
100
771
811
1MI8
116
156
Q55418
A
1
118
158
1
CYS
engineered mutation
ALA
1
1MI8
A
Q55418
UNP
381
3
1
CYS
engineered mutation
MET
50
1MI8
A
Q55418
UNP
430
52
1
linker
LEU
99
1MI8
A
Q55418
UNP
101
1
linker
GLU
100
1MI8
A
Q55418
UNP
102
1
linker
SER
101
1MI8
A
Q55418
UNP
103
1
linker
SER
102
1MI8
A
Q55418
UNP
104
1
linker
SER
103
1MI8
A
Q55418
UNP
105
1
linker
LEU
104
1MI8
A
Q55418
UNP
106
1
linker
GLN
105
1MI8
A
Q55418
UNP
107
1
linker
LEU
106
1MI8
A
Q55418
UNP
108
1
linker
SER
107
1MI8
A
Q55418
UNP
109
1
linker
PRO
108
1MI8
A
Q55418
UNP
110
1
linker
GLU
109
1MI8
A
Q55418
UNP
111
1
linker
ILE
110
1MI8
A
Q55418
UNP
112
1
linker
GLU
111
1MI8
A
Q55418
UNP
113
1
linker
LYS
112
1MI8
A
Q55418
UNP
114
1
linker
LEU
113
1MI8
A
Q55418
UNP
115
1
linker
SER
114
1MI8
A
Q55418
UNP
116
1
linker
GLN
115
1MI8
A
Q55418
UNP
117
1
TYR
engineered mutation
SER
119
1MI8
A
Q55418
UNP
774
121
1
ASN
engineered mutation
ALA
154
1MI8
A
Q55418
UNP
809
156
4
3
2
2
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
2
A
ILE
4
A
SER
3
A
SER
5
A
ILE
118
A
ILE
120
A
THR
138
A
THR
140
A
ARG
47
A
ARG
49
A
THR
61
A
THR
63
A
THR
66
A
THR
68
A
ALA
69
A
ALA
71
A
ILE
2
A
ILE
4
A
SER
3
A
SER
5
A
ILE
118
A
ILE
120
A
THR
138
A
THR
140
A
HIS
92
A
HIS
94
A
PRO
96
A
PRO
98
A
LEU
7
A
LEU
9
A
SER
9
A
SER
11
A
ARG
16
A
ARG
18
A
SER
18
A
SER
20
A
GLU
29
A
GLU
31
A
ASN
34
A
ASN
36
A
LYS
39
A
LYS
41
A
LYS
44
A
LYS
46
A
ARG
74
A
ARG
76
A
THR
77
A
THR
79
A
GLY
80
A
GLY
82
A
ARG
83
A
ARG
85
A
ASN
144
A
ASN
146
A
ALA
147
A
ALA
149
A
ILE
150
A
ILE
152
A
HIS
153
A
HIS
155
154
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