0.026430
-0.008543
-0.000546
0.000000
0.027216
-0.009086
0.000000
0.000000
0.026655
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
70.350
83.050
72.090
37.836
38.615
39.845
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 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
To be published
0353
Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution
10.2210/pdb3lyh/pdb
pdb_00003lyh
100
1
Flat collimating mirror, toroid focusing mirror
CCD
2010-01-23
MARMOSAIC 325 mm CCD
Double crystal monochromator
MAD
M
x-ray
1
0.97915
1.0
0.97903
1.0
0.91162
1.0
BL9-2
SSRL
0.97915,0.97903,0.91162
SYNCHROTRON
SSRL BEAMLINE BL9-2
14133.674
Cobalamin (Vitamin B12) biosynthesis CbiX protein
2
man
polymer
18.015
water
217
nat
water
no
yes
G(MSE)TQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAY(MSE)ELAEPSLDTIVNRAKGQGVEQFTVVPLFL
AAGRHLRKDVPA(MSE)IERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH
GMTQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAYMELAEPSLDTIVNRAKGQGVEQFTVVPLFLAAGRHLRK
DVPAMIERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH
A,B
403199
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
ATCC 700491 / DSM 11845 / VT8
sample
Maqu_1136
351348
Marinobacter aquaeolei
562
Escherichia coli
HK100
Plasmid
SpeedET
1
1.85
33.34
VAPOR DIFFUSION, SITTING DROP
6.0
20.0000% PEG-6000, 0.1M MES pH 6.0, 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
2010-04-07
1
1
2011-07-13
1
2
2017-11-08
1
3
2019-07-17
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
2010-02-26
REL
REL
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.
HOH
126
2
HOH
HOH
126
A
HOH
127
2
HOH
HOH
127
A
HOH
128
2
HOH
HOH
128
A
HOH
2
2
HOH
HOH
129
A
HOH
130
2
HOH
HOH
130
A
HOH
4
2
HOH
HOH
131
A
HOH
132
2
HOH
HOH
132
A
HOH
133
2
HOH
HOH
133
A
HOH
5
2
HOH
HOH
134
A
HOH
135
2
HOH
HOH
135
A
HOH
136
2
HOH
HOH
136
A
HOH
137
2
HOH
HOH
137
A
HOH
138
2
HOH
HOH
138
A
HOH
139
2
HOH
HOH
139
A
HOH
7
2
HOH
HOH
140
A
HOH
8
2
HOH
HOH
141
A
HOH
142
2
HOH
HOH
142
A
HOH
9
2
HOH
HOH
143
A
HOH
144
2
HOH
HOH
144
A
HOH
10
2
HOH
HOH
145
A
HOH
146
2
HOH
HOH
146
A
HOH
147
2
HOH
HOH
147
A
HOH
148
2
HOH
HOH
148
A
HOH
12
2
HOH
HOH
149
A
HOH
150
2
HOH
HOH
150
A
HOH
151
2
HOH
HOH
151
A
HOH
14
2
HOH
HOH
152
A
HOH
15
2
HOH
HOH
153
A
HOH
19
2
HOH
HOH
154
A
HOH
155
2
HOH
HOH
155
A
HOH
156
2
HOH
HOH
156
A
HOH
24
2
HOH
HOH
157
A
HOH
25
2
HOH
HOH
158
A
HOH
26
2
HOH
HOH
159
A
HOH
28
2
HOH
HOH
160
A
HOH
161
2
HOH
HOH
161
A
HOH
162
2
HOH
HOH
162
A
HOH
29
2
HOH
HOH
163
A
HOH
31
2
HOH
HOH
164
A
HOH
165
2
HOH
HOH
165
A
HOH
36
2
HOH
HOH
166
A
HOH
167
2
HOH
HOH
167
A
HOH
40
2
HOH
HOH
168
A
HOH
169
2
HOH
HOH
169
A
HOH
48
2
HOH
HOH
170
A
HOH
49
2
HOH
HOH
171
A
HOH
51
2
HOH
HOH
172
A
HOH
52
2
HOH
HOH
173
A
HOH
174
2
HOH
HOH
174
A
HOH
175
2
HOH
HOH
175
A
HOH
54
2
HOH
HOH
176
A
HOH
55
2
HOH
HOH
177
A
HOH
56
2
HOH
HOH
178
A
HOH
179
2
HOH
HOH
179
A
HOH
180
2
HOH
HOH
180
A
HOH
181
2
HOH
HOH
181
A
HOH
182
2
HOH
HOH
182
A
HOH
183
2
HOH
HOH
183
A
HOH
184
2
HOH
HOH
184
A
HOH
59
2
HOH
HOH
185
A
HOH
186
2
HOH
HOH
186
A
HOH
63
2
HOH
HOH
187
A
HOH
64
2
HOH
HOH
188
A
HOH
66
2
HOH
HOH
189
A
HOH
67
2
HOH
HOH
190
A
HOH
69
2
HOH
HOH
191
A
HOH
70
2
HOH
HOH
192
A
HOH
71
2
HOH
HOH
193
A
HOH
194
2
HOH
HOH
194
A
HOH
195
2
HOH
HOH
195
A
HOH
196
2
HOH
HOH
196
A
HOH
197
2
HOH
HOH
197
A
HOH
74
2
HOH
HOH
198
A
HOH
75
2
HOH
HOH
199
A
HOH
76
2
HOH
HOH
200
A
HOH
201
2
HOH
HOH
201
A
HOH
202
2
HOH
HOH
202
A
HOH
77
2
HOH
HOH
203
A
HOH
204
2
HOH
HOH
204
A
HOH
205
2
HOH
HOH
205
A
HOH
206
2
HOH
HOH
206
A
HOH
207
2
HOH
HOH
207
A
HOH
208
2
HOH
HOH
208
A
HOH
80
2
HOH
HOH
209
A
HOH
210
2
HOH
HOH
210
A
HOH
81
2
HOH
HOH
211
A
HOH
85
2
HOH
HOH
212
A
HOH
213
2
HOH
HOH
213
A
HOH
214
2
HOH
HOH
214
A
HOH
88
2
HOH
HOH
215
A
HOH
216
2
HOH
HOH
216
A
HOH
217
2
HOH
HOH
217
A
HOH
89
2
HOH
HOH
218
A
HOH
90
2
HOH
HOH
219
A
HOH
93
2
HOH
HOH
220
A
HOH
95
2
HOH
HOH
221
A
HOH
96
2
HOH
HOH
222
A
HOH
98
2
HOH
HOH
223
A
HOH
100
2
HOH
HOH
224
A
HOH
101
2
HOH
HOH
225
A
HOH
103
2
HOH
HOH
226
A
HOH
105
2
HOH
HOH
227
A
HOH
108
2
HOH
HOH
228
A
HOH
109
2
HOH
HOH
229
A
HOH
110
2
HOH
HOH
230
A
HOH
111
2
HOH
HOH
231
A
HOH
114
2
HOH
HOH
232
A
HOH
116
2
HOH
HOH
233
A
HOH
117
2
HOH
HOH
234
A
HOH
118
2
HOH
HOH
235
A
HOH
122
2
HOH
HOH
236
A
HOH
123
2
HOH
HOH
237
A
HOH
125
2
HOH
HOH
238
A
HOH
1
2
HOH
HOH
126
B
HOH
3
2
HOH
HOH
127
B
HOH
6
2
HOH
HOH
128
B
HOH
129
2
HOH
HOH
129
B
HOH
11
2
HOH
HOH
130
B
HOH
131
2
HOH
HOH
131
B
HOH
13
2
HOH
HOH
132
B
HOH
16
2
HOH
HOH
133
B
HOH
134
2
HOH
HOH
134
B
HOH
17
2
HOH
HOH
135
B
HOH
18
2
HOH
HOH
136
B
HOH
20
2
HOH
HOH
137
B
HOH
21
2
HOH
HOH
138
B
HOH
22
2
HOH
HOH
139
B
HOH
140
2
HOH
HOH
140
B
HOH
141
2
HOH
HOH
141
B
HOH
23
2
HOH
HOH
142
B
HOH
143
2
HOH
HOH
143
B
HOH
27
2
HOH
HOH
144
B
HOH
145
2
HOH
HOH
145
B
HOH
30
2
HOH
HOH
146
B
HOH
32
2
HOH
HOH
147
B
HOH
33
2
HOH
HOH
148
B
HOH
149
2
HOH
HOH
149
B
HOH
34
2
HOH
HOH
150
B
HOH
35
2
HOH
HOH
151
B
HOH
152
2
HOH
HOH
152
B
HOH
153
2
HOH
HOH
153
B
HOH
154
2
HOH
HOH
154
B
HOH
37
2
HOH
HOH
155
B
HOH
38
2
HOH
HOH
156
B
HOH
157
2
HOH
HOH
157
B
HOH
158
2
HOH
HOH
158
B
HOH
159
2
HOH
HOH
159
B
HOH
160
2
HOH
HOH
160
B
HOH
39
2
HOH
HOH
161
B
HOH
41
2
HOH
HOH
162
B
HOH
163
2
HOH
HOH
163
B
HOH
164
2
HOH
HOH
164
B
HOH
42
2
HOH
HOH
165
B
HOH
166
2
HOH
HOH
166
B
HOH
43
2
HOH
HOH
167
B
HOH
168
2
HOH
HOH
168
B
HOH
44
2
HOH
HOH
169
B
HOH
170
2
HOH
HOH
170
B
HOH
171
2
HOH
HOH
171
B
HOH
172
2
HOH
HOH
172
B
HOH
173
2
HOH
HOH
173
B
HOH
45
2
HOH
HOH
174
B
HOH
46
2
HOH
HOH
175
B
HOH
176
2
HOH
HOH
176
B
HOH
177
2
HOH
HOH
177
B
HOH
178
2
HOH
HOH
178
B
HOH
47
2
HOH
HOH
179
B
HOH
50
2
HOH
HOH
180
B
HOH
53
2
HOH
HOH
181
B
HOH
57
2
HOH
HOH
182
B
HOH
58
2
HOH
HOH
183
B
HOH
60
2
HOH
HOH
184
B
HOH
185
2
HOH
HOH
185
B
HOH
61
2
HOH
HOH
186
B
HOH
187
2
HOH
HOH
187
B
HOH
188
2
HOH
HOH
188
B
HOH
189
2
HOH
HOH
189
B
HOH
190
2
HOH
HOH
190
B
HOH
191
2
HOH
HOH
191
B
HOH
192
2
HOH
HOH
192
B
HOH
193
2
HOH
HOH
193
B
HOH
62
2
HOH
HOH
194
B
HOH
65
2
HOH
HOH
195
B
HOH
68
2
HOH
HOH
196
B
HOH
72
2
HOH
HOH
197
B
HOH
198
2
HOH
HOH
198
B
HOH
199
2
HOH
HOH
199
B
HOH
200
2
HOH
HOH
200
B
HOH
73
2
HOH
HOH
201
B
HOH
78
2
HOH
HOH
202
B
HOH
203
2
HOH
HOH
203
B
HOH
79
2
HOH
HOH
204
B
HOH
82
2
HOH
HOH
205
B
HOH
83
2
HOH
HOH
206
B
HOH
84
2
HOH
HOH
207
B
HOH
86
2
HOH
HOH
208
B
HOH
209
2
HOH
HOH
209
B
HOH
87
2
HOH
HOH
210
B
HOH
211
2
HOH
HOH
211
B
HOH
212
2
HOH
HOH
212
B
HOH
91
2
HOH
HOH
213
B
HOH
92
2
HOH
HOH
214
B
HOH
215
2
HOH
HOH
215
B
HOH
94
2
HOH
HOH
216
B
HOH
97
2
HOH
HOH
217
B
HOH
99
2
HOH
HOH
218
B
HOH
102
2
HOH
HOH
219
B
HOH
104
2
HOH
HOH
220
B
HOH
106
2
HOH
HOH
221
B
HOH
107
2
HOH
HOH
222
B
HOH
112
2
HOH
HOH
223
B
HOH
113
2
HOH
HOH
224
B
HOH
115
2
HOH
HOH
225
B
HOH
119
2
HOH
HOH
226
B
HOH
120
2
HOH
HOH
227
B
HOH
121
2
HOH
HOH
228
B
HOH
124
2
HOH
HOH
229
B
n
1
0
A
n
2
1
A
n
3
2
A
n
4
3
A
PRO
4
n
5
PRO
4
A
HIS
5
n
6
HIS
5
A
GLN
6
n
7
GLN
6
A
ILE
7
n
8
ILE
7
A
ILE
8
n
9
ILE
8
A
LEU
9
n
10
LEU
9
A
LEU
10
n
11
LEU
10
A
ALA
11
n
12
ALA
11
A
HIS
12
n
13
HIS
12
A
GLY
13
n
14
GLY
13
A
SER
14
n
15
SER
14
A
SER
15
n
16
SER
15
A
ASP
16
n
17
ASP
16
A
ALA
17
n
18
ALA
17
A
ARG
18
n
19
ARG
18
A
TRP
19
n
20
TRP
19
A
CYS
20
n
21
CYS
20
A
GLU
21
n
22
GLU
21
A
THR
22
n
23
THR
22
A
PHE
23
n
24
PHE
23
A
GLU
24
n
25
GLU
24
A
LYS
25
n
26
LYS
25
A
LEU
26
n
27
LEU
26
A
ALA
27
n
28
ALA
27
A
GLU
28
n
29
GLU
28
A
PRO
29
n
30
PRO
29
A
THR
30
n
31
THR
30
A
VAL
31
n
32
VAL
31
A
GLU
32
n
33
GLU
32
A
SER
33
n
34
SER
33
A
ILE
34
n
35
ILE
34
A
GLU
35
n
36
GLU
35
A
ASN
36
n
37
ASN
36
A
ALA
37
n
38
ALA
37
A
ALA
38
n
39
ALA
38
A
ILE
39
n
40
ILE
39
A
ALA
40
n
41
ALA
40
A
TYR
41
n
42
TYR
41
A
MSE
42
n
43
MSE
42
A
GLU
43
n
44
GLU
43
A
LEU
44
n
45
LEU
44
A
ALA
45
n
46
ALA
45
A
GLU
46
n
47
GLU
46
A
PRO
47
n
48
PRO
47
A
SER
48
n
49
SER
48
A
LEU
49
n
50
LEU
49
A
ASP
50
n
51
ASP
50
A
THR
51
n
52
THR
51
A
ILE
52
n
53
ILE
52
A
VAL
53
n
54
VAL
53
A
ASN
54
n
55
ASN
54
A
ARG
55
n
56
ARG
55
A
ALA
56
n
57
ALA
56
A
LYS
57
n
58
LYS
57
A
GLY
58
n
59
GLY
58
A
GLN
59
n
60
GLN
59
A
GLY
60
n
61
GLY
60
A
VAL
61
n
62
VAL
61
A
GLU
62
n
63
GLU
62
A
GLN
63
n
64
GLN
63
A
PHE
64
n
65
PHE
64
A
THR
65
n
66
THR
65
A
VAL
66
n
67
VAL
66
A
VAL
67
n
68
VAL
67
A
PRO
68
n
69
PRO
68
A
LEU
69
n
70
LEU
69
A
PHE
70
n
71
PHE
70
A
LEU
71
n
72
LEU
71
A
ALA
72
n
73
ALA
72
A
ALA
73
n
74
ALA
73
A
GLY
74
n
75
GLY
74
A
ARG
75
n
76
ARG
75
A
HIS
76
n
77
HIS
76
A
LEU
77
n
78
LEU
77
A
ARG
78
n
79
ARG
78
A
LYS
79
n
80
LYS
79
A
ASP
80
n
81
ASP
80
A
VAL
81
n
82
VAL
81
A
PRO
82
n
83
PRO
82
A
ALA
83
n
84
ALA
83
A
MSE
84
n
85
MSE
84
A
ILE
85
n
86
ILE
85
A
GLU
86
n
87
GLU
86
A
ARG
87
n
88
ARG
87
A
LEU
88
n
89
LEU
88
A
GLU
89
n
90
GLU
89
A
ALA
90
n
91
ALA
90
A
GLU
91
n
92
GLU
91
A
HIS
92
n
93
HIS
92
A
GLY
93
n
94
GLY
93
A
VAL
94
n
95
VAL
94
A
THR
95
n
96
THR
95
A
ILE
96
n
97
ILE
96
A
ARG
97
n
98
ARG
97
A
LEU
98
n
99
LEU
98
A
ALA
99
n
100
ALA
99
A
GLU
100
n
101
GLU
100
A
PRO
101
n
102
PRO
101
A
ILE
102
n
103
ILE
102
A
GLY
103
n
104
GLY
103
A
LYS
104
n
105
LYS
104
A
ASN
105
n
106
ASN
105
A
PRO
106
n
107
PRO
106
A
ARG
107
n
108
ARG
107
A
LEU
108
n
109
LEU
108
A
GLY
109
n
110
GLY
109
A
LEU
110
n
111
LEU
110
A
ALA
111
n
112
ALA
111
A
ILE
112
n
113
ILE
112
A
ARG
113
n
114
ARG
113
A
ASP
114
n
115
ASP
114
A
VAL
115
n
116
VAL
115
A
VAL
116
n
117
VAL
116
A
LYS
117
n
118
LYS
117
A
GLU
118
n
119
GLU
118
A
GLU
119
n
120
GLU
119
A
LEU
120
n
121
LEU
120
A
GLU
121
n
122
GLU
121
A
ARG
122
n
123
ARG
122
A
SER
123
n
124
SER
123
A
n
125
124
A
n
126
125
A
n
1
0
B
n
2
1
B
n
3
2
B
GLN
3
n
4
GLN
3
B
PRO
4
n
5
PRO
4
B
HIS
5
n
6
HIS
5
B
GLN
6
n
7
GLN
6
B
ILE
7
n
8
ILE
7
B
ILE
8
n
9
ILE
8
B
LEU
9
n
10
LEU
9
B
LEU
10
n
11
LEU
10
B
ALA
11
n
12
ALA
11
B
HIS
12
n
13
HIS
12
B
GLY
13
n
14
GLY
13
B
SER
14
n
15
SER
14
B
SER
15
n
16
SER
15
B
ASP
16
n
17
ASP
16
B
ALA
17
n
18
ALA
17
B
ARG
18
n
19
ARG
18
B
TRP
19
n
20
TRP
19
B
CYS
20
n
21
CYS
20
B
GLU
21
n
22
GLU
21
B
THR
22
n
23
THR
22
B
PHE
23
n
24
PHE
23
B
GLU
24
n
25
GLU
24
B
LYS
25
n
26
LYS
25
B
LEU
26
n
27
LEU
26
B
ALA
27
n
28
ALA
27
B
GLU
28
n
29
GLU
28
B
PRO
29
n
30
PRO
29
B
THR
30
n
31
THR
30
B
VAL
31
n
32
VAL
31
B
GLU
32
n
33
GLU
32
B
SER
33
n
34
SER
33
B
ILE
34
n
35
ILE
34
B
GLU
35
n
36
GLU
35
B
ASN
36
n
37
ASN
36
B
ALA
37
n
38
ALA
37
B
ALA
38
n
39
ALA
38
B
ILE
39
n
40
ILE
39
B
ALA
40
n
41
ALA
40
B
TYR
41
n
42
TYR
41
B
MSE
42
n
43
MSE
42
B
GLU
43
n
44
GLU
43
B
LEU
44
n
45
LEU
44
B
ALA
45
n
46
ALA
45
B
GLU
46
n
47
GLU
46
B
PRO
47
n
48
PRO
47
B
SER
48
n
49
SER
48
B
LEU
49
n
50
LEU
49
B
ASP
50
n
51
ASP
50
B
THR
51
n
52
THR
51
B
ILE
52
n
53
ILE
52
B
VAL
53
n
54
VAL
53
B
ASN
54
n
55
ASN
54
B
ARG
55
n
56
ARG
55
B
ALA
56
n
57
ALA
56
B
LYS
57
n
58
LYS
57
B
GLY
58
n
59
GLY
58
B
GLN
59
n
60
GLN
59
B
GLY
60
n
61
GLY
60
B
VAL
61
n
62
VAL
61
B
GLU
62
n
63
GLU
62
B
GLN
63
n
64
GLN
63
B
PHE
64
n
65
PHE
64
B
THR
65
n
66
THR
65
B
VAL
66
n
67
VAL
66
B
VAL
67
n
68
VAL
67
B
PRO
68
n
69
PRO
68
B
LEU
69
n
70
LEU
69
B
PHE
70
n
71
PHE
70
B
LEU
71
n
72
LEU
71
B
ALA
72
n
73
ALA
72
B
ALA
73
n
74
ALA
73
B
GLY
74
n
75
GLY
74
B
n
76
75
B
HIS
76
n
77
HIS
76
B
LEU
77
n
78
LEU
77
B
ARG
78
n
79
ARG
78
B
LYS
79
n
80
LYS
79
B
ASP
80
n
81
ASP
80
B
VAL
81
n
82
VAL
81
B
PRO
82
n
83
PRO
82
B
ALA
83
n
84
ALA
83
B
MSE
84
n
85
MSE
84
B
ILE
85
n
86
ILE
85
B
GLU
86
n
87
GLU
86
B
ARG
87
n
88
ARG
87
B
LEU
88
n
89
LEU
88
B
GLU
89
n
90
GLU
89
B
ALA
90
n
91
ALA
90
B
GLU
91
n
92
GLU
91
B
HIS
92
n
93
HIS
92
B
GLY
93
n
94
GLY
93
B
VAL
94
n
95
VAL
94
B
THR
95
n
96
THR
95
B
ILE
96
n
97
ILE
96
B
ARG
97
n
98
ARG
97
B
LEU
98
n
99
LEU
98
B
ALA
99
n
100
ALA
99
B
GLU
100
n
101
GLU
100
B
PRO
101
n
102
PRO
101
B
ILE
102
n
103
ILE
102
B
GLY
103
n
104
GLY
103
B
LYS
104
n
105
LYS
104
B
ASN
105
n
106
ASN
105
B
PRO
106
n
107
PRO
106
B
ARG
107
n
108
ARG
107
B
LEU
108
n
109
LEU
108
B
GLY
109
n
110
GLY
109
B
LEU
110
n
111
LEU
110
B
ALA
111
n
112
ALA
111
B
ILE
112
n
113
ILE
112
B
ARG
113
n
114
ARG
113
B
ASP
114
n
115
ASP
114
B
VAL
115
n
116
VAL
115
B
VAL
116
n
117
VAL
116
B
LYS
117
n
118
LYS
117
B
GLU
118
n
119
GLU
118
B
GLU
119
n
120
GLU
119
B
LEU
120
n
121
LEU
120
B
GLU
121
n
122
GLU
121
B
ARG
122
n
123
ARG
122
B
SER
123
n
124
SER
123
B
GLU
124
n
125
GLU
124
B
HIS
125
n
126
HIS
125
B
0.5134
-0.0765
-0.0744
0.6021
0.5339
1.3116
0.0552
0.0504
-0.0094
0.0255
-0.0138
-0.0205
0.0567
0.0637
-0.0414
0.0133
0.0097
0.0024
0.0150
0.0025
0.0141
refined
43.7798
33.6772
7.6424
X-RAY DIFFRACTION
0.6571
0.1883
0.2532
0.5340
0.6019
1.0500
-0.0482
-0.0020
0.0908
0.0107
-0.0246
0.0282
-0.0381
-0.0396
0.0728
0.0172
-0.0009
-0.0051
0.0121
0.0056
0.0282
refined
34.0782
48.4636
19.2297
X-RAY DIFFRACTION
A
4
A
123
X-RAY DIFFRACTION
1
B
3
B
125
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
2
dimeric
4150
-30
11340
A
MSE
42
SELENOMETHIONINE
A
MSE
43
MET
A
MSE
84
SELENOMETHIONINE
A
MSE
85
MET
B
MSE
42
SELENOMETHIONINE
B
MSE
43
MET
B
MSE
84
SELENOMETHIONINE
B
MSE
85
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
ALA
40
A
O
ALA
41
A
N
ALA
11
A
N
ALA
12
A
N
ILE
8
A
N
ILE
9
A
O
VAL
67
A
O
VAL
68
A
N
VAL
66
A
N
VAL
67
A
O
ARG
97
A
O
ARG
98
B
O
ALA
38
B
O
ALA
39
B
N
LEU
9
B
N
LEU
10
B
N
ILE
8
B
N
ILE
9
B
O
VAL
67
B
O
VAL
68
B
N
VAL
66
B
N
VAL
67
B
O
ARG
97
B
O
ARG
98
1
A
CG
PRO
4
A
CG
PRO
5
1
Y
1
A
CD
PRO
4
A
CD
PRO
5
1
Y
1
A
CG
GLU
35
A
CG
GLU
36
1
Y
1
A
CD
GLU
35
A
CD
GLU
36
1
Y
1
A
OE1
GLU
35
A
OE1
GLU
36
1
Y
1
A
OE2
GLU
35
A
OE2
GLU
36
1
Y
1
A
CD
ARG
75
A
CD
ARG
76
1
Y
1
A
NE
ARG
75
A
NE
ARG
76
1
Y
1
A
CZ
ARG
75
A
CZ
ARG
76
1
Y
1
A
NH1
ARG
75
A
NH1
ARG
76
1
Y
1
A
NH2
ARG
75
A
NH2
ARG
76
1
Y
1
A
CG
GLU
121
A
CG
GLU
122
1
Y
1
A
CD
GLU
121
A
CD
GLU
122
1
Y
1
A
OE1
GLU
121
A
OE1
GLU
122
1
Y
1
A
OE2
GLU
121
A
OE2
GLU
122
1
Y
1
A
CG
ARG
122
A
CG
ARG
123
1
Y
1
A
CD
ARG
122
A
CD
ARG
123
1
Y
1
A
NE
ARG
122
A
NE
ARG
123
1
Y
1
A
CZ
ARG
122
A
CZ
ARG
123
1
Y
1
A
NH1
ARG
122
A
NH1
ARG
123
1
Y
1
A
NH2
ARG
122
A
NH2
ARG
123
1
Y
1
B
CG
GLN
3
B
CG
GLN
4
1
Y
1
B
CD
GLN
3
B
CD
GLN
4
1
Y
1
B
OE1
GLN
3
B
OE1
GLN
4
1
Y
1
B
NE2
GLN
3
B
NE2
GLN
4
1
Y
1
B
CD
ARG
18
B
CD
ARG
19
1
Y
1
B
NE
ARG
18
B
NE
ARG
19
1
Y
1
B
CZ
ARG
18
B
CZ
ARG
19
1
Y
1
B
NH1
ARG
18
B
NH1
ARG
19
1
Y
1
B
NH2
ARG
18
B
NH2
ARG
19
1
Y
1
B
CD
LYS
25
B
CD
LYS
26
1
Y
1
B
CE
LYS
25
B
CE
LYS
26
1
Y
1
B
NZ
LYS
25
B
NZ
LYS
26
1
Y
1
B
CG
HIS
76
B
CG
HIS
77
1
Y
1
B
ND1
HIS
76
B
ND1
HIS
77
1
Y
1
B
CD2
HIS
76
B
CD2
HIS
77
1
Y
1
B
CE1
HIS
76
B
CE1
HIS
77
1
Y
1
B
NE2
HIS
76
B
NE2
HIS
77
1
Y
1
B
CG
LEU
77
B
CG
LEU
78
1
Y
1
B
CD1
LEU
77
B
CD1
LEU
78
1
Y
1
B
CD2
LEU
77
B
CD2
LEU
78
1
Y
1
B
CD
LYS
79
B
CD
LYS
80
1
Y
1
B
CE
LYS
79
B
CE
LYS
80
1
Y
1
B
NZ
LYS
79
B
NZ
LYS
80
1
Y
1
B
CG
HIS
125
B
CG
HIS
126
1
Y
1
B
ND1
HIS
125
B
ND1
HIS
126
1
Y
1
B
CD2
HIS
125
B
CD2
HIS
126
1
Y
1
B
CE1
HIS
125
B
CE1
HIS
126
1
Y
1
B
NE2
HIS
125
B
NE2
HIS
126
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
MSE
1
A
MSE
2
1
Y
1
A
THR
2
A
THR
3
1
Y
1
A
GLN
3
A
GLN
4
1
Y
1
A
GLU
124
A
GLU
125
1
Y
1
A
HIS
125
A
HIS
126
1
Y
1
B
GLY
0
B
GLY
1
1
Y
1
B
MSE
1
B
MSE
2
1
Y
1
B
THR
2
B
THR
3
1
Y
1
B
ARG
75
B
ARG
76
1
Y
1
3.08
0.50
120.30
123.38
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
78
78
78
N
1
A
LEU
44
73.10
-24.93
1
B
LEU
44
63.36
-11.73
60.53
19.754
2.43
0.070
-1.080
1.110
1.130
-1.160
-0.020
0.966
0.952
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.
0.209
0.170
0.172
1.600
29.618
1291
25860
5.000
96.460
1.00
0.30
4.121
0.065
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.103
0.102
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.600
29.618
217
2054
0
0
1837
0.016
0.022
1983
0.002
0.020
1339
1.645
1.977
2716
1.151
3.000
3303
6.166
5.000
272
36.175
24.419
86
13.339
15.000
348
16.660
15.000
14
0.097
0.200
319
0.007
0.021
2237
0.001
0.020
374
1.918
3.000
1262
0.527
3.000
503
3.135
5.000
2044
5.390
8.000
721
8.550
11.000
657
0.231
0.252
1.639
77
1729
1806
20
91.580
1.60
29.618
3LYH
25860
0.054
1
3.300
96.700
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0102
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
George M. 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
Phil R. Evans
pre@mrc-lmb.cam.ac.uk
2009/03/31
Fortran_77
http://www.ccp4.ac.uk/dist/html/scala.html
SCALA
other
3.3.15
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.006
data reduction
MOSFLM
phasing
SHELXD
phasing
autoSHARP
Crystal structure of Putative cobalamin (vitamin B12) biosynthesis CbiX protein (YP_958415.1) from Marinobacter aquaeolei VT8 at 1.60 A resolution
1
N
N
1
N
N
2
N
N
2
N
N
A
ASP
16
A
ASP
17
HELX_P
A
ILE
34
A
ILE
35
1
1
19
A
SER
48
A
SER
49
HELX_P
A
GLN
59
A
GLN
60
1
2
12
A
GLY
74
A
GLY
75
HELX_P
A
GLY
93
A
GLY
94
1
3
20
A
PRO
101
A
PRO
102
HELX_P
A
LYS
104
A
LYS
105
5
4
4
A
ASN
105
A
ASN
106
HELX_P
A
SER
123
A
SER
124
1
5
19
B
ASP
16
B
ASP
17
HELX_P
B
ILE
34
B
ILE
35
1
6
19
B
SER
48
B
SER
49
HELX_P
B
GLN
59
B
GLN
60
1
7
12
B
HIS
76
B
HIS
77
HELX_P
B
GLY
93
B
GLY
94
1
8
18
B
PRO
101
B
PRO
102
HELX_P
B
LYS
104
B
LYS
105
5
9
4
B
ASN
105
B
ASN
106
HELX_P
B
HIS
125
B
HIS
126
1
10
21
covale
1.330
both
A
TYR
41
A
C
TYR
42
1_555
A
MSE
42
A
N
MSE
43
1_555
covale
1.328
both
A
MSE
42
A
C
MSE
43
1_555
A
GLU
43
A
N
GLU
44
1_555
covale
1.334
both
A
ALA
83
A
C
ALA
84
1_555
A
MSE
84
A
N
MSE
85
1_555
covale
1.334
both
A
MSE
84
A
C
MSE
85
1_555
A
ILE
85
A
N
ILE
86
1_555
covale
1.317
both
B
TYR
41
B
C
TYR
42
1_555
B
MSE
42
B
N
MSE
43
1_555
covale
1.338
both
B
MSE
42
B
C
MSE
43
1_555
B
GLU
43
B
N
GLU
44
1_555
covale
1.333
both
B
ALA
83
B
C
ALA
84
1_555
B
MSE
84
B
N
MSE
85
1_555
covale
1.339
both
B
MSE
84
B
C
MSE
85
1_555
B
ILE
85
B
N
ILE
86
1_555
LYASE
Putative cobalamin (vitamin B12) biosynthesis CbiX protein, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, LYASE
A
GLU
46
A
GLU
47
1
A
PRO
47
A
PRO
48
-0.32
B
GLN
3
B
GLN
4
1
B
PRO
4
B
PRO
5
-22.75
B
GLU
46
B
GLU
47
1
B
PRO
47
B
PRO
48
2.63
A1TZQ9_MARAV
UNP
1
1
A1TZQ9
MTQPHQIILLAHGSSDARWCETFEKLAEPTVESIENAAIAYMELAEPSLDTIVNRAKGQGVEQFTVVPLFLAAGRHLRKD
VPAMIERLEAEHGVTIRLAEPIGKNPRLGLAIRDVVKEELERSEH
1
125
3LYH
1
125
A1TZQ9
A
1
2
126
1
125
3LYH
1
125
A1TZQ9
B
1
2
126
1
expression tag
GLY
0
3LYH
A
A1TZQ9
UNP
1
2
expression tag
GLY
0
3LYH
B
A1TZQ9
UNP
1
4
4
parallel
parallel
parallel
parallel
parallel
parallel
A
ALA
38
A
ALA
39
A
TYR
41
A
TYR
42
A
HIS
5
A
HIS
6
A
ALA
11
A
ALA
12
A
GLN
63
A
GLN
64
A
PRO
68
A
PRO
69
A
THR
95
A
THR
96
A
LEU
98
A
LEU
99
B
ALA
37
B
ALA
38
B
TYR
41
B
TYR
42
B
HIS
5
B
HIS
6
B
ALA
11
B
ALA
12
B
GLN
63
B
GLN
64
B
PRO
68
B
PRO
69
B
THR
95
B
THR
96
B
LEU
98
B
LEU
99
1
P 1