0.017334
0.000000
0.000000
0.000000
0.015788
0.000000
0.000000
0.000000
0.012186
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
57.690
63.340
82.060
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
Cl -1
35.453
CHLORIDE ION
non-polymer
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 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
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
Crystal structure of a DinB-like Protein (NP_389123.1) from BACILLUS SUBTILIS at 2.30 A resolution
10.2210/pdb3dka/pdb
pdb_00003dka
100
1
Flat mirror (vertical focusing)
CCD
2008-05-14
MARMOSAIC 325 mm CCD
Single crystal Si(111) bent monochromator (horizontal focusing)
MAD
M
x-ray
1
0.91837
1.0
0.97956
1.0
0.97904
1.0
BL11-1
SSRL
0.91837,0.97956,0.97904
SYNCHROTRON
SSRL BEAMLINE BL11-1
18109.627
DinB-like Protein
2
man
polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
98
nat
water
no
yes
G(MSE)CQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETS(MSE)SAEELVKHILTSFHLFANVIKEGNASPFQNKQ
EETETDLNVLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLA(MSE)EHEIHHKGNLFVYVRE(MSE)G
HTELPFYQQR(MSE)
GMCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLN
VLAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM
A,B
389728
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
sample
NP_389123.1, yjoA, BSU12410
1423
Bacillus subtilis
Escherichia Coli
HK100
Plasmid
SpeedET
1
2.07
40.57
VAPOR DIFFUSION, SITTING DROP
5.6
0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
software
software
struct_conn
database_2
struct_ref_seq_dif
repository
Initial release
Advisory
Version format compliance
Refinement description
Data collection
Derived calculations
Refinement description
Database references
1
0
2008-08-19
1
1
2011-07-13
1
2
2017-10-25
1
3
2019-07-24
1
4
2023-02-01
_software.classification
_software.name
_software.classification
_software.contact_author
_software.contact_author_email
_software.language
_software.location
_software.name
_software.type
_software.version
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Y
RCSB
Y
RCSB
2008-06-24
REL
REL
CL
CHLORIDE ION
HOH
water
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
CL
1
2
CL
CL
155
A
HOH
2
3
HOH
HOH
156
A
HOH
4
3
HOH
HOH
157
A
HOH
5
3
HOH
HOH
158
A
HOH
6
3
HOH
HOH
159
A
HOH
8
3
HOH
HOH
160
A
HOH
10
3
HOH
HOH
161
A
HOH
12
3
HOH
HOH
162
A
HOH
13
3
HOH
HOH
163
A
HOH
18
3
HOH
HOH
164
A
HOH
19
3
HOH
HOH
165
A
HOH
21
3
HOH
HOH
166
A
HOH
22
3
HOH
HOH
167
A
HOH
25
3
HOH
HOH
168
A
HOH
26
3
HOH
HOH
169
A
HOH
28
3
HOH
HOH
170
A
HOH
30
3
HOH
HOH
171
A
HOH
31
3
HOH
HOH
172
A
HOH
32
3
HOH
HOH
173
A
HOH
33
3
HOH
HOH
174
A
HOH
34
3
HOH
HOH
175
A
HOH
39
3
HOH
HOH
176
A
HOH
40
3
HOH
HOH
177
A
HOH
41
3
HOH
HOH
178
A
HOH
51
3
HOH
HOH
179
A
HOH
57
3
HOH
HOH
180
A
HOH
60
3
HOH
HOH
181
A
HOH
62
3
HOH
HOH
182
A
HOH
63
3
HOH
HOH
183
A
HOH
66
3
HOH
HOH
184
A
HOH
67
3
HOH
HOH
185
A
HOH
68
3
HOH
HOH
186
A
HOH
69
3
HOH
HOH
187
A
HOH
70
3
HOH
HOH
188
A
HOH
71
3
HOH
HOH
189
A
HOH
73
3
HOH
HOH
190
A
HOH
76
3
HOH
HOH
191
A
HOH
78
3
HOH
HOH
192
A
HOH
81
3
HOH
HOH
193
A
HOH
82
3
HOH
HOH
194
A
HOH
83
3
HOH
HOH
195
A
HOH
84
3
HOH
HOH
196
A
HOH
87
3
HOH
HOH
197
A
HOH
88
3
HOH
HOH
198
A
HOH
89
3
HOH
HOH
199
A
HOH
93
3
HOH
HOH
200
A
HOH
95
3
HOH
HOH
201
A
HOH
97
3
HOH
HOH
202
A
HOH
98
3
HOH
HOH
203
A
HOH
99
3
HOH
HOH
204
A
HOH
3
3
HOH
HOH
155
B
HOH
7
3
HOH
HOH
156
B
HOH
9
3
HOH
HOH
157
B
HOH
11
3
HOH
HOH
158
B
HOH
14
3
HOH
HOH
159
B
HOH
15
3
HOH
HOH
160
B
HOH
16
3
HOH
HOH
161
B
HOH
17
3
HOH
HOH
162
B
HOH
20
3
HOH
HOH
163
B
HOH
23
3
HOH
HOH
164
B
HOH
24
3
HOH
HOH
165
B
HOH
27
3
HOH
HOH
166
B
HOH
29
3
HOH
HOH
167
B
HOH
35
3
HOH
HOH
168
B
HOH
36
3
HOH
HOH
169
B
HOH
37
3
HOH
HOH
170
B
HOH
38
3
HOH
HOH
171
B
HOH
42
3
HOH
HOH
172
B
HOH
43
3
HOH
HOH
173
B
HOH
44
3
HOH
HOH
174
B
HOH
45
3
HOH
HOH
175
B
HOH
46
3
HOH
HOH
176
B
HOH
47
3
HOH
HOH
177
B
HOH
48
3
HOH
HOH
178
B
HOH
49
3
HOH
HOH
179
B
HOH
50
3
HOH
HOH
180
B
HOH
52
3
HOH
HOH
181
B
HOH
53
3
HOH
HOH
182
B
HOH
54
3
HOH
HOH
183
B
HOH
55
3
HOH
HOH
184
B
HOH
56
3
HOH
HOH
185
B
HOH
58
3
HOH
HOH
186
B
HOH
59
3
HOH
HOH
187
B
HOH
61
3
HOH
HOH
188
B
HOH
64
3
HOH
HOH
189
B
HOH
65
3
HOH
HOH
190
B
HOH
72
3
HOH
HOH
191
B
HOH
74
3
HOH
HOH
192
B
HOH
75
3
HOH
HOH
193
B
HOH
77
3
HOH
HOH
194
B
HOH
79
3
HOH
HOH
195
B
HOH
80
3
HOH
HOH
196
B
HOH
85
3
HOH
HOH
197
B
HOH
86
3
HOH
HOH
198
B
HOH
90
3
HOH
HOH
199
B
HOH
91
3
HOH
HOH
200
B
HOH
92
3
HOH
HOH
201
B
HOH
94
3
HOH
HOH
202
B
HOH
96
3
HOH
HOH
203
B
n
1
0
A
n
2
1
A
n
3
2
A
n
4
3
A
n
5
4
A
ASN
5
n
6
ASN
5
A
GLN
6
n
7
GLN
6
A
ILE
7
n
8
ILE
7
A
VAL
8
n
9
VAL
8
A
SER
9
n
10
SER
9
A
HIS
10
n
11
HIS
10
A
PHE
11
n
12
PHE
11
A
LEU
12
n
13
LEU
12
A
SER
13
n
14
SER
13
A
HIS
14
n
15
HIS
14
A
ARG
15
n
16
ARG
15
A
ASN
16
n
17
ASN
16
A
VAL
17
n
18
VAL
17
A
THR
18
n
19
THR
18
A
ASN
19
n
20
ASN
19
A
GLU
20
n
21
GLU
20
A
LEU
21
n
22
LEU
21
A
ALA
22
n
23
ALA
22
A
GLU
23
n
24
GLU
23
A
LYS
24
n
25
LYS
24
A
ILE
25
n
26
ILE
25
A
SER
26
n
27
SER
26
A
LYS
27
n
28
LYS
27
A
ASP
28
n
29
ASP
28
A
HIS
29
n
30
HIS
29
A
TYR
30
n
31
TYR
30
A
SER
31
n
32
SER
31
A
TYR
32
n
33
TYR
32
A
LYS
33
n
34
LYS
33
A
PRO
34
n
35
PRO
34
A
ALA
35
n
36
ALA
35
A
GLU
36
n
37
GLU
36
A
THR
37
n
38
THR
37
A
SER
38
n
39
SER
38
A
MSE
39
n
40
MSE
39
A
SER
40
n
41
SER
40
A
ALA
41
n
42
ALA
41
A
GLU
42
n
43
GLU
42
A
GLU
43
n
44
GLU
43
A
LEU
44
n
45
LEU
44
A
VAL
45
n
46
VAL
45
A
LYS
46
n
47
LYS
46
A
HIS
47
n
48
HIS
47
A
ILE
48
n
49
ILE
48
A
LEU
49
n
50
LEU
49
A
THR
50
n
51
THR
50
A
SER
51
n
52
SER
51
A
PHE
52
n
53
PHE
52
A
HIS
53
n
54
HIS
53
A
LEU
54
n
55
LEU
54
A
PHE
55
n
56
PHE
55
A
ALA
56
n
57
ALA
56
A
ASN
57
n
58
ASN
57
A
VAL
58
n
59
VAL
58
A
ILE
59
n
60
ILE
59
A
LYS
60
n
61
LYS
60
A
GLU
61
n
62
GLU
61
A
GLY
62
n
63
GLY
62
A
ASN
63
n
64
ASN
63
A
ALA
64
n
65
ALA
64
A
SER
65
n
66
SER
65
A
PRO
66
n
67
PRO
66
A
PHE
67
n
68
PHE
67
A
GLN
68
n
69
GLN
68
A
ASN
69
n
70
ASN
69
A
n
71
70
A
n
72
71
A
n
73
72
A
n
74
73
A
THR
74
n
75
THR
74
A
GLU
75
n
76
GLU
75
A
THR
76
n
77
THR
76
A
ASP
77
n
78
ASP
77
A
LEU
78
n
79
LEU
78
A
ASN
79
n
80
ASN
79
A
VAL
80
n
81
VAL
80
A
LEU
81
n
82
LEU
81
A
ALA
82
n
83
ALA
82
A
LYS
83
n
84
LYS
83
A
THR
84
n
85
THR
84
A
TYR
85
n
86
TYR
85
A
THR
86
n
87
THR
86
A
GLU
87
n
88
GLU
87
A
LYS
88
n
89
LYS
88
A
THR
89
n
90
THR
89
A
VAL
90
n
91
VAL
90
A
ALA
91
n
92
ALA
91
A
ILE
92
n
93
ILE
92
A
LEU
93
n
94
LEU
93
A
GLU
94
n
95
GLU
94
A
GLN
95
n
96
GLN
95
A
LEU
96
n
97
LEU
96
A
THR
97
n
98
THR
97
A
GLU
98
n
99
GLU
98
A
GLU
99
n
100
GLU
99
A
GLN
100
n
101
GLN
100
A
LEU
101
n
102
LEU
101
A
ASP
102
n
103
ASP
102
A
ARG
103
n
104
ARG
103
A
GLU
104
n
105
GLU
104
A
ILE
105
n
106
ILE
105
A
ASP
106
n
107
ASP
106
A
n
108
107
A
n
109
108
A
n
110
109
A
ALA
110
n
111
ALA
110
A
PHE
111
n
112
PHE
111
A
GLY
112
n
113
GLY
112
A
ARG
113
n
114
ARG
113
A
LYS
114
n
115
LYS
114
A
VAL
115
n
116
VAL
115
A
THR
116
n
117
THR
116
A
GLY
117
n
118
GLY
117
A
ARG
118
n
119
ARG
118
A
ALA
119
n
120
ALA
119
A
LEU
120
n
121
LEU
120
A
LEU
121
n
122
LEU
121
A
GLN
122
n
123
GLN
122
A
LEU
123
n
124
LEU
123
A
ALA
124
n
125
ALA
124
A
MSE
125
n
126
MSE
125
A
GLU
126
n
127
GLU
126
A
HIS
127
n
128
HIS
127
A
GLU
128
n
129
GLU
128
A
ILE
129
n
130
ILE
129
A
HIS
130
n
131
HIS
130
A
HIS
131
n
132
HIS
131
A
LYS
132
n
133
LYS
132
A
GLY
133
n
134
GLY
133
A
ASN
134
n
135
ASN
134
A
LEU
135
n
136
LEU
135
A
PHE
136
n
137
PHE
136
A
VAL
137
n
138
VAL
137
A
TYR
138
n
139
TYR
138
A
VAL
139
n
140
VAL
139
A
ARG
140
n
141
ARG
140
A
GLU
141
n
142
GLU
141
A
MSE
142
n
143
MSE
142
A
GLY
143
n
144
GLY
143
A
HIS
144
n
145
HIS
144
A
THR
145
n
146
THR
145
A
GLU
146
n
147
GLU
146
A
LEU
147
n
148
LEU
147
A
PRO
148
n
149
PRO
148
A
PHE
149
n
150
PHE
149
A
TYR
150
n
151
TYR
150
A
GLN
151
n
152
GLN
151
A
GLN
152
n
153
GLN
152
A
ARG
153
n
154
ARG
153
A
MSE
154
n
155
MSE
154
A
n
1
0
B
n
2
1
B
n
3
2
B
n
4
3
B
n
5
4
B
ASN
5
n
6
ASN
5
B
GLN
6
n
7
GLN
6
B
ILE
7
n
8
ILE
7
B
VAL
8
n
9
VAL
8
B
SER
9
n
10
SER
9
B
HIS
10
n
11
HIS
10
B
PHE
11
n
12
PHE
11
B
LEU
12
n
13
LEU
12
B
SER
13
n
14
SER
13
B
HIS
14
n
15
HIS
14
B
ARG
15
n
16
ARG
15
B
ASN
16
n
17
ASN
16
B
VAL
17
n
18
VAL
17
B
THR
18
n
19
THR
18
B
ASN
19
n
20
ASN
19
B
GLU
20
n
21
GLU
20
B
LEU
21
n
22
LEU
21
B
ALA
22
n
23
ALA
22
B
GLU
23
n
24
GLU
23
B
LYS
24
n
25
LYS
24
B
ILE
25
n
26
ILE
25
B
SER
26
n
27
SER
26
B
LYS
27
n
28
LYS
27
B
ASP
28
n
29
ASP
28
B
HIS
29
n
30
HIS
29
B
TYR
30
n
31
TYR
30
B
SER
31
n
32
SER
31
B
TYR
32
n
33
TYR
32
B
LYS
33
n
34
LYS
33
B
PRO
34
n
35
PRO
34
B
ALA
35
n
36
ALA
35
B
GLU
36
n
37
GLU
36
B
THR
37
n
38
THR
37
B
SER
38
n
39
SER
38
B
MSE
39
n
40
MSE
39
B
SER
40
n
41
SER
40
B
ALA
41
n
42
ALA
41
B
GLU
42
n
43
GLU
42
B
GLU
43
n
44
GLU
43
B
LEU
44
n
45
LEU
44
B
VAL
45
n
46
VAL
45
B
LYS
46
n
47
LYS
46
B
HIS
47
n
48
HIS
47
B
ILE
48
n
49
ILE
48
B
LEU
49
n
50
LEU
49
B
THR
50
n
51
THR
50
B
SER
51
n
52
SER
51
B
PHE
52
n
53
PHE
52
B
HIS
53
n
54
HIS
53
B
LEU
54
n
55
LEU
54
B
PHE
55
n
56
PHE
55
B
ALA
56
n
57
ALA
56
B
ASN
57
n
58
ASN
57
B
VAL
58
n
59
VAL
58
B
ILE
59
n
60
ILE
59
B
LYS
60
n
61
LYS
60
B
GLU
61
n
62
GLU
61
B
GLY
62
n
63
GLY
62
B
ASN
63
n
64
ASN
63
B
ALA
64
n
65
ALA
64
B
SER
65
n
66
SER
65
B
PRO
66
n
67
PRO
66
B
PHE
67
n
68
PHE
67
B
GLN
68
n
69
GLN
68
B
ASN
69
n
70
ASN
69
B
LYS
70
n
71
LYS
70
B
GLN
71
n
72
GLN
71
B
GLU
72
n
73
GLU
72
B
GLU
73
n
74
GLU
73
B
THR
74
n
75
THR
74
B
GLU
75
n
76
GLU
75
B
THR
76
n
77
THR
76
B
ASP
77
n
78
ASP
77
B
LEU
78
n
79
LEU
78
B
ASN
79
n
80
ASN
79
B
VAL
80
n
81
VAL
80
B
LEU
81
n
82
LEU
81
B
ALA
82
n
83
ALA
82
B
LYS
83
n
84
LYS
83
B
THR
84
n
85
THR
84
B
TYR
85
n
86
TYR
85
B
THR
86
n
87
THR
86
B
GLU
87
n
88
GLU
87
B
LYS
88
n
89
LYS
88
B
THR
89
n
90
THR
89
B
VAL
90
n
91
VAL
90
B
ALA
91
n
92
ALA
91
B
ILE
92
n
93
ILE
92
B
LEU
93
n
94
LEU
93
B
GLU
94
n
95
GLU
94
B
GLN
95
n
96
GLN
95
B
LEU
96
n
97
LEU
96
B
THR
97
n
98
THR
97
B
GLU
98
n
99
GLU
98
B
GLU
99
n
100
GLU
99
B
GLN
100
n
101
GLN
100
B
LEU
101
n
102
LEU
101
B
ASP
102
n
103
ASP
102
B
ARG
103
n
104
ARG
103
B
GLU
104
n
105
GLU
104
B
ILE
105
n
106
ILE
105
B
ASP
106
n
107
ASP
106
B
LEU
107
n
108
LEU
107
B
THR
108
n
109
THR
108
B
n
110
109
B
n
111
110
B
n
112
111
B
n
113
112
B
n
114
113
B
LYS
114
n
115
LYS
114
B
VAL
115
n
116
VAL
115
B
THR
116
n
117
THR
116
B
GLY
117
n
118
GLY
117
B
ARG
118
n
119
ARG
118
B
ALA
119
n
120
ALA
119
B
LEU
120
n
121
LEU
120
B
LEU
121
n
122
LEU
121
B
GLN
122
n
123
GLN
122
B
LEU
123
n
124
LEU
123
B
ALA
124
n
125
ALA
124
B
MSE
125
n
126
MSE
125
B
GLU
126
n
127
GLU
126
B
HIS
127
n
128
HIS
127
B
GLU
128
n
129
GLU
128
B
ILE
129
n
130
ILE
129
B
HIS
130
n
131
HIS
130
B
HIS
131
n
132
HIS
131
B
LYS
132
n
133
LYS
132
B
GLY
133
n
134
GLY
133
B
ASN
134
n
135
ASN
134
B
LEU
135
n
136
LEU
135
B
PHE
136
n
137
PHE
136
B
VAL
137
n
138
VAL
137
B
TYR
138
n
139
TYR
138
B
VAL
139
n
140
VAL
139
B
ARG
140
n
141
ARG
140
B
GLU
141
n
142
GLU
141
B
MSE
142
n
143
MSE
142
B
GLY
143
n
144
GLY
143
B
HIS
144
n
145
HIS
144
B
THR
145
n
146
THR
145
B
GLU
146
n
147
GLU
146
B
LEU
147
n
148
LEU
147
B
PRO
148
n
149
PRO
148
B
PHE
149
n
150
PHE
149
B
TYR
150
n
151
TYR
150
B
GLN
151
n
152
GLN
151
B
GLN
152
n
153
GLN
152
B
ARG
153
n
154
ARG
153
B
n
155
154
B
0.7332
0.2212
-0.2770
1.0220
-0.4726
2.4037
-0.0481
0.0144
0.0834
-0.0617
0.0822
0.1071
-0.1075
-0.1458
-0.0341
-0.0656
0.0059
-0.0026
-0.0319
-0.0036
-0.0223
refined
17.7978
36.2709
18.3858
X-RAY DIFFRACTION
1.3254
-0.3565
-1.5279
0.2585
-0.0198
2.9029
-0.0561
-0.0141
0.0528
0.1019
0.0465
-0.1325
0.0032
0.0979
0.0096
-0.0432
-0.0303
-0.0031
-0.0686
-0.0216
-0.0105
refined
37.8085
37.5655
28.0478
X-RAY DIFFRACTION
A
5
A
6
A
154
A
155
X-RAY DIFFRACTION
1
B
5
B
6
B
153
B
154
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
2
dimeric
1880
-11
14180
A
MSE
39
SELENOMETHIONINE
A
MSE
40
MET
A
MSE
125
SELENOMETHIONINE
A
MSE
126
MET
A
MSE
142
SELENOMETHIONINE
A
MSE
143
MET
A
MSE
154
SELENOMETHIONINE
A
MSE
155
MET
B
MSE
39
SELENOMETHIONINE
B
MSE
40
MET
B
MSE
125
SELENOMETHIONINE
B
MSE
126
MET
B
MSE
142
SELENOMETHIONINE
B
MSE
143
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
N
ILE
105
A
N
ILE
106
A
O
VAL
115
A
O
VAL
116
B
N
ILE
105
B
N
ILE
106
B
O
VAL
115
B
O
VAL
116
1
A
CD
GLN
6
A
CD
GLN
7
1
Y
1
A
OE1
GLN
6
A
OE1
GLN
7
1
Y
1
A
NE2
GLN
6
A
NE2
GLN
7
1
Y
1
A
CG
ASN
69
A
CG
ASN
70
1
Y
1
A
OD1
ASN
69
A
OD1
ASN
70
1
Y
1
A
ND2
ASN
69
A
ND2
ASN
70
1
Y
1
A
OG1
THR
74
A
OG1
THR
75
1
Y
1
A
CG2
THR
74
A
CG2
THR
75
1
Y
1
A
CG
ASP
106
A
CG
ASP
107
1
Y
1
A
OD1
ASP
106
A
OD1
ASP
107
1
Y
1
A
OD2
ASP
106
A
OD2
ASP
107
1
Y
1
A
CG
PHE
111
A
CG
PHE
112
1
Y
1
A
CD1
PHE
111
A
CD1
PHE
112
1
Y
1
A
CD2
PHE
111
A
CD2
PHE
112
1
Y
1
A
CE1
PHE
111
A
CE1
PHE
112
1
Y
1
A
CE2
PHE
111
A
CE2
PHE
112
1
Y
1
A
CZ
PHE
111
A
CZ
PHE
112
1
Y
1
A
CD
ARG
113
A
CD
ARG
114
1
Y
1
A
NE
ARG
113
A
NE
ARG
114
1
Y
1
A
CZ
ARG
113
A
CZ
ARG
114
1
Y
1
A
NH1
ARG
113
A
NH1
ARG
114
1
Y
1
A
NH2
ARG
113
A
NH2
ARG
114
1
Y
1
B
CG
GLN
6
B
CG
GLN
7
1
Y
1
B
CD
GLN
6
B
CD
GLN
7
1
Y
1
B
OE1
GLN
6
B
OE1
GLN
7
1
Y
1
B
NE2
GLN
6
B
NE2
GLN
7
1
Y
1
B
CG
ASN
69
B
CG
ASN
70
1
Y
1
B
OD1
ASN
69
B
OD1
ASN
70
1
Y
1
B
ND2
ASN
69
B
ND2
ASN
70
1
Y
1
B
CG
LYS
70
B
CG
LYS
71
1
Y
1
B
CD
LYS
70
B
CD
LYS
71
1
Y
1
B
CE
LYS
70
B
CE
LYS
71
1
Y
1
B
NZ
LYS
70
B
NZ
LYS
71
1
Y
1
B
CG
GLN
71
B
CG
GLN
72
1
Y
1
B
CD
GLN
71
B
CD
GLN
72
1
Y
1
B
OE1
GLN
71
B
OE1
GLN
72
1
Y
1
B
NE2
GLN
71
B
NE2
GLN
72
1
Y
1
B
CG
GLU
72
B
CG
GLU
73
1
Y
1
B
CD
GLU
72
B
CD
GLU
73
1
Y
1
B
OE1
GLU
72
B
OE1
GLU
73
1
Y
1
B
OE2
GLU
72
B
OE2
GLU
73
1
Y
1
B
OG1
THR
74
B
OG1
THR
75
1
Y
1
B
CG2
THR
74
B
CG2
THR
75
1
Y
1
B
CG
LYS
114
B
CG
LYS
115
1
Y
1
B
CD
LYS
114
B
CD
LYS
115
1
Y
1
B
CE
LYS
114
B
CE
LYS
115
1
Y
1
B
NZ
LYS
114
B
NZ
LYS
115
1
Y
1
B
CG
ARG
153
B
CG
ARG
154
1
Y
1
B
CD
ARG
153
B
CD
ARG
154
1
Y
1
B
NE
ARG
153
B
NE
ARG
154
1
Y
1
B
CZ
ARG
153
B
CZ
ARG
154
1
Y
1
B
NH1
ARG
153
B
NH1
ARG
154
1
Y
1
B
NH2
ARG
153
B
NH2
ARG
154
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
MSE
1
A
MSE
2
1
Y
1
A
CYS
2
A
CYS
3
1
Y
1
A
GLN
3
A
GLN
4
1
Y
1
A
SER
4
A
SER
5
1
Y
1
A
LYS
70
A
LYS
71
1
Y
1
A
GLN
71
A
GLN
72
1
Y
1
A
GLU
72
A
GLU
73
1
Y
1
A
GLU
73
A
GLU
74
1
Y
1
A
LEU
107
A
LEU
108
1
Y
1
A
THR
108
A
THR
109
1
Y
1
A
SER
109
A
SER
110
1
Y
1
B
GLY
0
B
GLY
1
1
Y
1
B
MSE
1
B
MSE
2
1
Y
1
B
CYS
2
B
CYS
3
1
Y
1
B
GLN
3
B
GLN
4
1
Y
1
B
SER
4
B
SER
5
1
Y
1
B
SER
109
B
SER
110
1
Y
1
B
ALA
110
B
ALA
111
1
Y
1
B
PHE
111
B
PHE
112
1
Y
1
B
GLY
112
B
GLY
113
1
Y
1
B
ARG
113
B
ARG
114
1
Y
1
B
MSE
154
B
MSE
155
1
Y
1
A
ARG
113
-122.61
-143.72
1
A
LYS
114
-173.60
146.20
1
B
ASN
69
-69.96
95.31
27.260
2.390
0.000
0.000
-0.470
0.000
-1.920
0.930
0.893
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE
INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY
OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75
FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET
INCORPORATION.
3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
0.269
0.217
0.219
2.300
29.566
677
13568
5.000
97.560
15.654
0.193
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.437
0.273
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
2.300
29.566
98
2387
1
0
2288
0.009
0.021
2343
0.006
0.020
1532
1.073
1.945
3168
0.839
3.000
3763
4.557
5.000
286
33.959
25.043
117
13.550
15.000
418
10.103
15.000
9
0.065
0.200
364
0.003
0.020
2587
0.001
0.020
450
0.192
0.200
519
0.170
0.200
1538
0.172
0.200
1131
0.087
0.200
1140
0.142
0.200
89
0.105
0.200
16
0.225
0.200
18
0.243
0.200
5
1.304
3.000
1511
0.211
3.000
577
2.082
5.000
2308
3.402
8.000
953
4.632
11.000
858
1
A
1
798
X-RAY DIFFRACTION
TIGHT POSITIONAL
0.070
0.100
1
A
1
1007
X-RAY DIFFRACTION
MEDIUM POSITIONAL
0.250
0.400
1
A
1
798
X-RAY DIFFRACTION
TIGHT THERMAL
0.070
0.500
1
A
1
1007
X-RAY DIFFRACTION
MEDIUM THERMAL
0.280
1.000
0.289
0.263
2.380
58
1225
1283
15
96.030
34.972
2.30
29.566
3DKA
13596
-3.00
0.097
1
7.300
3.63
95.900
0.571
2.30
2.38
1.58
4548
2313
1
90.50
0.462
2.38
2.48
1.9
5203
2619
1
96.10
0.378
2.48
2.59
2.4
4812
2441
1
96.40
0.280
2.59
2.73
3.0
5069
2554
1
96.00
0.214
2.73
2.90
3.9
4885
2460
1
96.00
0.163
2.90
3.12
5.0
4873
2468
1
97.20
0.107
3.12
3.43
7.6
4973
2501
1
96.80
0.060
3.43
3.93
12.0
4994
2523
1
96.40
0.040
3.93
4.93
16.6
4955
2499
1
97.10
0.035
4.93
29.57
18.5
5051
2562
1
96.50
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.2.0019
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
George Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html
XSCALE
package
data extraction
PDB
sw-help@rcsb.rutgers.edu
September 10, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.004
data reduction
XDS
phasing
SHELXD
phasing
autoSHARP
Y
Crystal structure of a dinb-like protein (yjoa, bsu12410) from bacillus subtilis at 2.30 A resolution
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
A
ASN
5
A
ASN
6
HELX_P
A
GLU
23
A
GLU
24
1
1
19
A
SER
40
A
SER
41
HELX_P
A
GLY
62
A
GLY
63
1
2
23
A
ALA
64
A
ALA
65
HELX_P
A
GLN
68
A
GLN
69
5
3
5
A
ASP
77
A
ASP
78
HELX_P
A
GLN
95
A
GLN
96
1
4
19
A
THR
97
A
THR
98
HELX_P
A
ARG
103
A
ARG
104
1
5
7
A
GLY
117
A
GLY
118
HELX_P
A
MSE
142
A
MSE
143
1
6
26
B
ASN
5
B
ASN
6
HELX_P
B
LYS
24
B
LYS
25
1
7
20
B
ILE
25
B
ILE
26
HELX_P
B
TYR
30
B
TYR
31
5
8
6
B
SER
40
B
SER
41
HELX_P
B
GLY
62
B
GLY
63
1
9
23
B
ALA
64
B
ALA
65
HELX_P
B
GLN
68
B
GLN
69
5
10
5
B
ASP
77
B
ASP
78
HELX_P
B
GLU
94
B
GLU
95
1
11
18
B
THR
97
B
THR
98
HELX_P
B
ARG
103
B
ARG
104
1
12
7
B
GLY
117
B
GLY
118
HELX_P
B
MSE
142
B
MSE
143
1
13
26
covale
1.332
both
A
SER
38
A
C
SER
39
1_555
A
MSE
39
A
N
MSE
40
1_555
covale
1.328
both
A
MSE
39
A
C
MSE
40
1_555
A
SER
40
A
N
SER
41
1_555
covale
1.329
both
A
ALA
124
A
C
ALA
125
1_555
A
MSE
125
A
N
MSE
126
1_555
covale
1.329
both
A
MSE
125
A
C
MSE
126
1_555
A
GLU
126
A
N
GLU
127
1_555
covale
1.332
both
A
GLU
141
A
C
GLU
142
1_555
A
MSE
142
A
N
MSE
143
1_555
covale
1.333
both
A
MSE
142
A
C
MSE
143
1_555
A
GLY
143
A
N
GLY
144
1_555
covale
1.334
both
A
ARG
153
A
C
ARG
154
1_555
A
MSE
154
A
N
MSE
155
1_555
covale
1.334
both
B
SER
38
B
C
SER
39
1_555
B
MSE
39
B
N
MSE
40
1_555
covale
1.326
both
B
MSE
39
B
C
MSE
40
1_555
B
SER
40
B
N
SER
41
1_555
covale
1.333
both
B
ALA
124
B
C
ALA
125
1_555
B
MSE
125
B
N
MSE
126
1_555
covale
1.325
both
B
MSE
125
B
C
MSE
126
1_555
B
GLU
126
B
N
GLU
127
1_555
covale
1.331
both
B
GLU
141
B
C
GLU
142
1_555
B
MSE
142
B
N
MSE
143
1_555
covale
1.333
both
B
MSE
142
B
C
MSE
143
1_555
B
GLY
143
B
N
GLY
144
1_555
UNKNOWN FUNCTION
Dinb/yfit-like putative metalloenzyme fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function
A
B
A
B
A
B
A
5
A
5
A
67
A
67
2
B
5
B
5
B
67
B
67
2
A
68
A
68
A
69
A
69
4
B
68
B
68
B
69
B
69
4
A
70
A
70
A
152
A
152
2
B
70
B
70
B
152
B
152
2
YJOA_BACSU
UNP
1
1
O34334
MCQSNQIVSHFLSHRNVTNELAEKISKDHYSYKPAETSMSAEELVKHILTSFHLFANVIKEGNASPFQNKQEETETDLNV
LAKTYTEKTVAILEQLTEEQLDREIDLTSAFGRKVTGRALLQLAMEHEIHHKGNLFVYVREMGHTELPFYQQRM
1
154
3DKA
1
154
O34334
A
1
2
155
1
154
3DKA
1
154
O34334
B
1
2
155
1
expression tag
GLY
0
3DKA
A
O34334
UNP
1
2
expression tag
GLY
0
3DKA
B
O34334
UNP
1
2
2
anti-parallel
anti-parallel
A
GLU
104
A
GLU
105
A
ILE
105
A
ILE
106
A
VAL
115
A
VAL
116
A
THR
116
A
THR
117
B
GLU
104
B
GLU
105
B
ILE
105
B
ILE
106
B
VAL
115
B
VAL
116
B
THR
116
B
THR
117
19
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