0.006156
0.000000
0.000000
0.000000
0.006156
0.000000
0.000000
0.000000
0.006156
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
48
90.000
90.000
90.000
162.440
162.440
162.440
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
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
O4 S -2
96.063
SULFATE ION
non-polymer
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 a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution
10.2210/pdb3sc3/pdb
pdb_00003sc3
100
1
Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
CCD
2008-11-15
MARMOSAIC 325 mm CCD
single crystal Si(111) bent
SINGLE WAVELENGTH
M
x-ray
1
0.97799
1.0
BL11-1
SSRL
0.97799
SYNCHROTRON
SSRL BEAMLINE BL11-1
25509.047
Putative DNA replication regulator Hda
2
man
polymer
96.063
SULFATE ION
5
syn
non-polymer
Regulatory inactivation of DnaA Hda protein
no
yes
GVHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASISTA
LLEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASP(MSE)EAGFVLPDLVSR(MSE)HWGLTY
QLQP(MSE)(MSE)DDEKLAALQRRAA(MSE)RGLQLPEDVGRFLLNR(MSE)ARDLRTLFDVLDRLDKAS(MSE)VHQR
KLTIPFVKE(MSE)LRL
GVHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASISTA
LLEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDD
EKLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQRKLTIPFVKEMLRL
A,B
396931
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
SB2B
sample
SAMA_14OCT04_CONTIG53_REVISED_GENE1514, Sama_1916
326297
Shewanella amazonensis
562
Escherichia Coli
HK100
Plasmid
SpeedET
1
3.50
64.86
VAPOR DIFFUSION, SITTING DROP
7.5
1.26M (NH4)2SO4, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI:Biology
pdbx_struct_assembly_auth_evidence
software
citation_author
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Author supporting evidence
Refinement description
Database references
Database references
Derived calculations
1
0
2011-07-13
1
1
2017-10-25
1
2
2018-01-24
1
3
2023-02-01
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal structure of a putative DNA replication regulator Hda (Sama_1916) from Shewanella amazonensis SB2B at 1.75 A resolution - CDP and Mg2+ bound
Y
RCSB
Y
RCSB
2011-06-06
REL
REL
SO4
SULFATE ION
THE CONSTRUCT (RESIDUES 18-241) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
SO4
1
2
SO4
SO4
1
A
SO4
2
2
SO4
SO4
2
A
SO4
3
2
SO4
SO4
3
B
SO4
4
2
SO4
SO4
4
B
SO4
5
2
SO4
SO4
5
B
n
1
0
A
n
2
18
A
n
3
19
A
n
4
20
A
n
5
21
A
n
6
22
A
n
7
23
A
n
8
24
A
n
9
25
A
n
10
26
A
n
11
27
A
n
12
28
A
n
13
29
A
TYR
30
n
14
TYR
30
A
PRO
31
n
15
PRO
31
A
ALA
32
n
16
ALA
32
A
ALA
33
n
17
ALA
33
A
GLY
34
n
18
GLY
34
A
ASN
35
n
19
ASN
35
A
ASP
36
n
20
ASP
36
A
GLU
37
n
21
GLU
37
A
LEU
38
n
22
LEU
38
A
ILE
39
n
23
ILE
39
A
GLY
40
n
24
GLY
40
A
ALA
41
n
25
ALA
41
A
LEU
42
n
26
LEU
42
A
LYS
43
n
27
LYS
43
A
SER
44
n
28
SER
44
A
ALA
45
n
29
ALA
45
A
ALA
46
n
30
ALA
46
A
SER
47
n
31
SER
47
A
GLY
48
n
32
GLY
48
A
ASP
49
n
33
ASP
49
A
GLY
50
n
34
GLY
50
A
VAL
51
n
35
VAL
51
A
GLN
52
n
36
GLN
52
A
ALA
53
n
37
ALA
53
A
ILE
54
n
38
ILE
54
A
TYR
55
n
39
TYR
55
A
LEU
56
n
40
LEU
56
A
TRP
57
n
41
TRP
57
A
GLY
58
n
42
GLY
58
A
PRO
59
n
43
PRO
59
A
VAL
60
n
44
VAL
60
A
LYS
61
n
45
LYS
61
A
SER
62
n
46
SER
62
A
GLY
63
n
47
GLY
63
A
ARG
64
n
48
ARG
64
A
THR
65
n
49
THR
65
A
HIS
66
n
50
HIS
66
A
LEU
67
n
51
LEU
67
A
ILE
68
n
52
ILE
68
A
HIS
69
n
53
HIS
69
A
ALA
70
n
54
ALA
70
A
ALA
71
n
55
ALA
71
A
CYS
72
n
56
CYS
72
A
ALA
73
n
57
ALA
73
A
ARG
74
n
58
ARG
74
A
ALA
75
n
59
ALA
75
A
ASN
76
n
60
ASN
76
A
GLU
77
n
61
GLU
77
A
LEU
78
n
62
LEU
78
A
GLU
79
n
63
GLU
79
A
ARG
80
n
64
ARG
80
A
ARG
81
n
65
ARG
81
A
SER
82
n
66
SER
82
A
PHE
83
n
67
PHE
83
A
TYR
84
n
68
TYR
84
A
ILE
85
n
69
ILE
85
A
PRO
86
n
70
PRO
86
A
LEU
87
n
71
LEU
87
A
GLY
88
n
72
GLY
88
A
ILE
89
n
73
ILE
89
A
HIS
90
n
74
HIS
90
A
ALA
91
n
75
ALA
91
A
SER
92
n
76
SER
92
A
ILE
93
n
77
ILE
93
A
SER
94
n
78
SER
94
A
THR
95
n
79
THR
95
A
ALA
96
n
80
ALA
96
A
LEU
97
n
81
LEU
97
A
LEU
98
n
82
LEU
98
A
GLU
99
n
83
GLU
99
A
GLY
100
n
84
GLY
100
A
LEU
101
n
85
LEU
101
A
GLU
102
n
86
GLU
102
A
GLN
103
n
87
GLN
103
A
PHE
104
n
88
PHE
104
A
ASP
105
n
89
ASP
105
A
LEU
106
n
90
LEU
106
A
ILE
107
n
91
ILE
107
A
CYS
108
n
92
CYS
108
A
ILE
109
n
93
ILE
109
A
ASP
110
n
94
ASP
110
A
ASP
111
n
95
ASP
111
A
VAL
112
n
96
VAL
112
A
ASP
113
n
97
ASP
113
A
ALA
114
n
98
ALA
114
A
VAL
115
n
99
VAL
115
A
ALA
116
n
100
ALA
116
A
GLY
117
n
101
GLY
117
A
HIS
118
n
102
HIS
118
A
PRO
119
n
103
PRO
119
A
LEU
120
n
104
LEU
120
A
TRP
121
n
105
TRP
121
A
GLU
122
n
106
GLU
122
A
GLU
123
n
107
GLU
123
A
ALA
124
n
108
ALA
124
A
ILE
125
n
109
ILE
125
A
PHE
126
n
110
PHE
126
A
ASP
127
n
111
ASP
127
A
LEU
128
n
112
LEU
128
A
TYR
129
n
113
TYR
129
A
ASN
130
n
114
ASN
130
A
ARG
131
n
115
ARG
131
A
VAL
132
n
116
VAL
132
A
ALA
133
n
117
ALA
133
A
GLU
134
n
118
GLU
134
A
GLN
135
n
119
GLN
135
A
LYS
136
n
120
LYS
136
A
ARG
137
n
121
ARG
137
A
GLY
138
n
122
GLY
138
A
SER
139
n
123
SER
139
A
LEU
140
n
124
LEU
140
A
ILE
141
n
125
ILE
141
A
VAL
142
n
126
VAL
142
A
SER
143
n
127
SER
143
A
ALA
144
n
128
ALA
144
A
SER
145
n
129
SER
145
A
ALA
146
n
130
ALA
146
A
SER
147
n
131
SER
147
A
PRO
148
n
132
PRO
148
A
MSE
149
n
133
MSE
149
A
GLU
150
n
134
GLU
150
A
ALA
151
n
135
ALA
151
A
GLY
152
n
136
GLY
152
A
PHE
153
n
137
PHE
153
A
VAL
154
n
138
VAL
154
A
LEU
155
n
139
LEU
155
A
PRO
156
n
140
PRO
156
A
ASP
157
n
141
ASP
157
A
LEU
158
n
142
LEU
158
A
VAL
159
n
143
VAL
159
A
SER
160
n
144
SER
160
A
ARG
161
n
145
ARG
161
A
MSE
162
n
146
MSE
162
A
HIS
163
n
147
HIS
163
A
TRP
164
n
148
TRP
164
A
GLY
165
n
149
GLY
165
A
LEU
166
n
150
LEU
166
A
THR
167
n
151
THR
167
A
TYR
168
n
152
TYR
168
A
GLN
169
n
153
GLN
169
A
LEU
170
n
154
LEU
170
A
GLN
171
n
155
GLN
171
A
PRO
172
n
156
PRO
172
A
MSE
173
n
157
MSE
173
A
MSE
174
n
158
MSE
174
A
ASP
175
n
159
ASP
175
A
ASP
176
n
160
ASP
176
A
GLU
177
n
161
GLU
177
A
LYS
178
n
162
LYS
178
A
LEU
179
n
163
LEU
179
A
ALA
180
n
164
ALA
180
A
ALA
181
n
165
ALA
181
A
LEU
182
n
166
LEU
182
A
GLN
183
n
167
GLN
183
A
ARG
184
n
168
ARG
184
A
ARG
185
n
169
ARG
185
A
ALA
186
n
170
ALA
186
A
ALA
187
n
171
ALA
187
A
MSE
188
n
172
MSE
188
A
ARG
189
n
173
ARG
189
A
GLY
190
n
174
GLY
190
A
LEU
191
n
175
LEU
191
A
GLN
192
n
176
GLN
192
A
LEU
193
n
177
LEU
193
A
PRO
194
n
178
PRO
194
A
GLU
195
n
179
GLU
195
A
ASP
196
n
180
ASP
196
A
VAL
197
n
181
VAL
197
A
GLY
198
n
182
GLY
198
A
ARG
199
n
183
ARG
199
A
PHE
200
n
184
PHE
200
A
LEU
201
n
185
LEU
201
A
LEU
202
n
186
LEU
202
A
ASN
203
n
187
ASN
203
A
ARG
204
n
188
ARG
204
A
MSE
205
n
189
MSE
205
A
ALA
206
n
190
ALA
206
A
ARG
207
n
191
ARG
207
A
ASP
208
n
192
ASP
208
A
LEU
209
n
193
LEU
209
A
ARG
210
n
194
ARG
210
A
THR
211
n
195
THR
211
A
LEU
212
n
196
LEU
212
A
PHE
213
n
197
PHE
213
A
ASP
214
n
198
ASP
214
A
VAL
215
n
199
VAL
215
A
LEU
216
n
200
LEU
216
A
ASP
217
n
201
ASP
217
A
ARG
218
n
202
ARG
218
A
LEU
219
n
203
LEU
219
A
ASP
220
n
204
ASP
220
A
LYS
221
n
205
LYS
221
A
ALA
222
n
206
ALA
222
A
SER
223
n
207
SER
223
A
MSE
224
n
208
MSE
224
A
VAL
225
n
209
VAL
225
A
HIS
226
n
210
HIS
226
A
GLN
227
n
211
GLN
227
A
ARG
228
n
212
ARG
228
A
LYS
229
n
213
LYS
229
A
LEU
230
n
214
LEU
230
A
THR
231
n
215
THR
231
A
ILE
232
n
216
ILE
232
A
PRO
233
n
217
PRO
233
A
PHE
234
n
218
PHE
234
A
VAL
235
n
219
VAL
235
A
LYS
236
n
220
LYS
236
A
GLU
237
n
221
GLU
237
A
MSE
238
n
222
MSE
238
A
LEU
239
n
223
LEU
239
A
ARG
240
n
224
ARG
240
A
LEU
241
n
225
LEU
241
A
n
1
0
B
n
2
18
B
n
3
19
B
n
4
20
B
n
5
21
B
n
6
22
B
n
7
23
B
n
8
24
B
n
9
25
B
n
10
26
B
n
11
27
B
n
12
28
B
n
13
29
B
n
14
30
B
PRO
31
n
15
PRO
31
B
ALA
32
n
16
ALA
32
B
ALA
33
n
17
ALA
33
B
GLY
34
n
18
GLY
34
B
ASN
35
n
19
ASN
35
B
ASP
36
n
20
ASP
36
B
GLU
37
n
21
GLU
37
B
LEU
38
n
22
LEU
38
B
ILE
39
n
23
ILE
39
B
GLY
40
n
24
GLY
40
B
ALA
41
n
25
ALA
41
B
LEU
42
n
26
LEU
42
B
LYS
43
n
27
LYS
43
B
SER
44
n
28
SER
44
B
ALA
45
n
29
ALA
45
B
ALA
46
n
30
ALA
46
B
SER
47
n
31
SER
47
B
GLY
48
n
32
GLY
48
B
ASP
49
n
33
ASP
49
B
GLY
50
n
34
GLY
50
B
VAL
51
n
35
VAL
51
B
GLN
52
n
36
GLN
52
B
ALA
53
n
37
ALA
53
B
ILE
54
n
38
ILE
54
B
TYR
55
n
39
TYR
55
B
LEU
56
n
40
LEU
56
B
TRP
57
n
41
TRP
57
B
GLY
58
n
42
GLY
58
B
PRO
59
n
43
PRO
59
B
VAL
60
n
44
VAL
60
B
LYS
61
n
45
LYS
61
B
SER
62
n
46
SER
62
B
GLY
63
n
47
GLY
63
B
ARG
64
n
48
ARG
64
B
THR
65
n
49
THR
65
B
HIS
66
n
50
HIS
66
B
LEU
67
n
51
LEU
67
B
ILE
68
n
52
ILE
68
B
HIS
69
n
53
HIS
69
B
ALA
70
n
54
ALA
70
B
ALA
71
n
55
ALA
71
B
CYS
72
n
56
CYS
72
B
ALA
73
n
57
ALA
73
B
ARG
74
n
58
ARG
74
B
ALA
75
n
59
ALA
75
B
ASN
76
n
60
ASN
76
B
GLU
77
n
61
GLU
77
B
LEU
78
n
62
LEU
78
B
GLU
79
n
63
GLU
79
B
ARG
80
n
64
ARG
80
B
ARG
81
n
65
ARG
81
B
SER
82
n
66
SER
82
B
PHE
83
n
67
PHE
83
B
TYR
84
n
68
TYR
84
B
ILE
85
n
69
ILE
85
B
PRO
86
n
70
PRO
86
B
LEU
87
n
71
LEU
87
B
GLY
88
n
72
GLY
88
B
ILE
89
n
73
ILE
89
B
HIS
90
n
74
HIS
90
B
ALA
91
n
75
ALA
91
B
SER
92
n
76
SER
92
B
ILE
93
n
77
ILE
93
B
SER
94
n
78
SER
94
B
THR
95
n
79
THR
95
B
ALA
96
n
80
ALA
96
B
LEU
97
n
81
LEU
97
B
LEU
98
n
82
LEU
98
B
GLU
99
n
83
GLU
99
B
GLY
100
n
84
GLY
100
B
LEU
101
n
85
LEU
101
B
GLU
102
n
86
GLU
102
B
GLN
103
n
87
GLN
103
B
PHE
104
n
88
PHE
104
B
ASP
105
n
89
ASP
105
B
LEU
106
n
90
LEU
106
B
ILE
107
n
91
ILE
107
B
CYS
108
n
92
CYS
108
B
ILE
109
n
93
ILE
109
B
ASP
110
n
94
ASP
110
B
ASP
111
n
95
ASP
111
B
VAL
112
n
96
VAL
112
B
ASP
113
n
97
ASP
113
B
ALA
114
n
98
ALA
114
B
VAL
115
n
99
VAL
115
B
ALA
116
n
100
ALA
116
B
GLY
117
n
101
GLY
117
B
HIS
118
n
102
HIS
118
B
PRO
119
n
103
PRO
119
B
LEU
120
n
104
LEU
120
B
TRP
121
n
105
TRP
121
B
GLU
122
n
106
GLU
122
B
GLU
123
n
107
GLU
123
B
ALA
124
n
108
ALA
124
B
ILE
125
n
109
ILE
125
B
PHE
126
n
110
PHE
126
B
ASP
127
n
111
ASP
127
B
LEU
128
n
112
LEU
128
B
TYR
129
n
113
TYR
129
B
ASN
130
n
114
ASN
130
B
ARG
131
n
115
ARG
131
B
VAL
132
n
116
VAL
132
B
ALA
133
n
117
ALA
133
B
GLU
134
n
118
GLU
134
B
GLN
135
n
119
GLN
135
B
LYS
136
n
120
LYS
136
B
ARG
137
n
121
ARG
137
B
GLY
138
n
122
GLY
138
B
SER
139
n
123
SER
139
B
LEU
140
n
124
LEU
140
B
ILE
141
n
125
ILE
141
B
VAL
142
n
126
VAL
142
B
SER
143
n
127
SER
143
B
ALA
144
n
128
ALA
144
B
SER
145
n
129
SER
145
B
ALA
146
n
130
ALA
146
B
SER
147
n
131
SER
147
B
PRO
148
n
132
PRO
148
B
MSE
149
n
133
MSE
149
B
GLU
150
n
134
GLU
150
B
ALA
151
n
135
ALA
151
B
GLY
152
n
136
GLY
152
B
PHE
153
n
137
PHE
153
B
VAL
154
n
138
VAL
154
B
LEU
155
n
139
LEU
155
B
PRO
156
n
140
PRO
156
B
ASP
157
n
141
ASP
157
B
LEU
158
n
142
LEU
158
B
VAL
159
n
143
VAL
159
B
SER
160
n
144
SER
160
B
ARG
161
n
145
ARG
161
B
MSE
162
n
146
MSE
162
B
HIS
163
n
147
HIS
163
B
TRP
164
n
148
TRP
164
B
GLY
165
n
149
GLY
165
B
LEU
166
n
150
LEU
166
B
THR
167
n
151
THR
167
B
TYR
168
n
152
TYR
168
B
GLN
169
n
153
GLN
169
B
LEU
170
n
154
LEU
170
B
GLN
171
n
155
GLN
171
B
PRO
172
n
156
PRO
172
B
MSE
173
n
157
MSE
173
B
MSE
174
n
158
MSE
174
B
ASP
175
n
159
ASP
175
B
ASP
176
n
160
ASP
176
B
GLU
177
n
161
GLU
177
B
LYS
178
n
162
LYS
178
B
LEU
179
n
163
LEU
179
B
ALA
180
n
164
ALA
180
B
ALA
181
n
165
ALA
181
B
LEU
182
n
166
LEU
182
B
GLN
183
n
167
GLN
183
B
ARG
184
n
168
ARG
184
B
ARG
185
n
169
ARG
185
B
ALA
186
n
170
ALA
186
B
ALA
187
n
171
ALA
187
B
MSE
188
n
172
MSE
188
B
ARG
189
n
173
ARG
189
B
GLY
190
n
174
GLY
190
B
LEU
191
n
175
LEU
191
B
GLN
192
n
176
GLN
192
B
LEU
193
n
177
LEU
193
B
PRO
194
n
178
PRO
194
B
GLU
195
n
179
GLU
195
B
ASP
196
n
180
ASP
196
B
VAL
197
n
181
VAL
197
B
GLY
198
n
182
GLY
198
B
ARG
199
n
183
ARG
199
B
PHE
200
n
184
PHE
200
B
LEU
201
n
185
LEU
201
B
LEU
202
n
186
LEU
202
B
ASN
203
n
187
ASN
203
B
ARG
204
n
188
ARG
204
B
MSE
205
n
189
MSE
205
B
ALA
206
n
190
ALA
206
B
ARG
207
n
191
ARG
207
B
ASP
208
n
192
ASP
208
B
LEU
209
n
193
LEU
209
B
ARG
210
n
194
ARG
210
B
THR
211
n
195
THR
211
B
LEU
212
n
196
LEU
212
B
PHE
213
n
197
PHE
213
B
ASP
214
n
198
ASP
214
B
VAL
215
n
199
VAL
215
B
LEU
216
n
200
LEU
216
B
ASP
217
n
201
ASP
217
B
ARG
218
n
202
ARG
218
B
LEU
219
n
203
LEU
219
B
ASP
220
n
204
ASP
220
B
LYS
221
n
205
LYS
221
B
ALA
222
n
206
ALA
222
B
SER
223
n
207
SER
223
B
MSE
224
n
208
MSE
224
B
VAL
225
n
209
VAL
225
B
HIS
226
n
210
HIS
226
B
GLN
227
n
211
GLN
227
B
ARG
228
n
212
ARG
228
B
LYS
229
n
213
LYS
229
B
LEU
230
n
214
LEU
230
B
THR
231
n
215
THR
231
B
ILE
232
n
216
ILE
232
B
PRO
233
n
217
PRO
233
B
PHE
234
n
218
PHE
234
B
VAL
235
n
219
VAL
235
B
LYS
236
n
220
LYS
236
B
GLU
237
n
221
GLU
237
B
MSE
238
n
222
MSE
238
B
LEU
239
n
223
LEU
239
B
ARG
240
n
224
ARG
240
B
LEU
241
n
225
LEU
241
B
-0.1030
0.0296
0.0472
-0.0095
0.0889
0.0233
1.5144
1.5546
-1.2483
-0.8519
-0.0810
1.5361
0.1964
-0.6946
-0.0002
2.0440
-0.0410
0.5256
2.0654
-0.4757
2.4473
refined
40.3695
11.9674
117.9710
X-RAY DIFFRACTION
4.9755
-2.4450
-0.7820
6.7755
-0.6714
5.9025
0.1335
-0.5295
0.4594
0.6432
-0.0440
-0.0292
-0.4127
0.0451
0.0000
1.1118
0.0469
-0.0920
1.2424
-0.1298
1.2356
refined
60.5264
10.6813
116.9135
X-RAY DIFFRACTION
-0.0270
0.0921
0.0773
-0.1401
-0.0090
0.0139
-0.2857
0.0089
-1.1875
0.2794
1.6830
0.6906
1.0831
-2.5249
0.0000
1.6533
0.1643
-0.2828
2.3319
0.2733
1.7208
refined
39.8913
3.2278
120.2593
X-RAY DIFFRACTION
2.7534
-1.9910
-0.7890
4.7506
0.9134
4.4168
0.3077
-0.5373
-0.5023
0.4879
0.0453
-0.1312
0.2491
0.0864
-0.0000
1.4733
0.0352
0.1231
1.3581
0.2221
1.4010
refined
23.4539
0.2123
107.6912
X-RAY DIFFRACTION
0.1295
0.1149
-0.0697
0.0079
-0.0785
0.1402
-0.1811
-1.0869
0.4450
-0.1228
-0.0698
-2.0228
-0.7776
0.2292
-0.0001
1.7112
0.1255
0.0124
1.3271
0.0141
1.9525
refined
34.3426
28.9727
100.7788
X-RAY DIFFRACTION
4.2377
-0.1440
2.7663
5.0511
-0.6066
5.7466
-0.0583
-0.4185
0.4881
0.5908
0.1286
0.3744
-0.4097
-0.3926
0.0000
1.1468
0.1063
0.0739
1.0291
-0.0101
1.2708
refined
18.1056
21.1585
97.1512
X-RAY DIFFRACTION
0.0487
-0.1098
0.1071
-0.0964
-0.1666
-0.0594
0.4861
1.1096
-1.3206
-1.3070
-0.4221
-0.1880
-0.1396
0.8859
0.0000
1.5727
-0.0207
-0.0809
1.3832
0.2286
1.9200
refined
39.7281
24.7419
91.0132
X-RAY DIFFRACTION
2.6085
-0.0952
1.3343
5.1331
0.1765
4.0871
0.2495
0.6502
0.3763
-0.1276
-0.1686
0.1020
-0.0760
-0.0650
-0.0000
1.1462
-0.0151
0.1009
1.3187
0.1014
1.2355
refined
57.3607
12.8738
93.1299
X-RAY DIFFRACTION
A
30
A
35
X-RAY DIFFRACTION
1
chain A and resseq 30:35
A
36
A
168
X-RAY DIFFRACTION
2
chain A and resseq 36:168
A
169
A
175
X-RAY DIFFRACTION
3
chain A and resseq 169:175
A
176
A
241
X-RAY DIFFRACTION
4
chain A and resseq 176:241
B
31
B
38
X-RAY DIFFRACTION
5
chain B and resseq 31:38
B
39
B
168
X-RAY DIFFRACTION
6
chain B and resseq 39:168
B
169
B
175
X-RAY DIFFRACTION
7
chain B and resseq 169:175
B
176
B
241
X-RAY DIFFRACTION
8
chain B and resseq 176:241
author_and_software_defined_assembly
PISA
2
dimeric
gel filtration
light scattering
3310
-96
21000
A
MSE
149
SELENOMETHIONINE
A
MSE
133
MET
A
MSE
162
SELENOMETHIONINE
A
MSE
146
MET
A
MSE
173
SELENOMETHIONINE
A
MSE
157
MET
A
MSE
174
SELENOMETHIONINE
A
MSE
158
MET
A
MSE
188
SELENOMETHIONINE
A
MSE
172
MET
A
MSE
205
SELENOMETHIONINE
A
MSE
189
MET
A
MSE
224
SELENOMETHIONINE
A
MSE
208
MET
A
MSE
238
SELENOMETHIONINE
A
MSE
222
MET
B
MSE
149
SELENOMETHIONINE
B
MSE
133
MET
B
MSE
162
SELENOMETHIONINE
B
MSE
146
MET
B
MSE
173
SELENOMETHIONINE
B
MSE
157
MET
B
MSE
174
SELENOMETHIONINE
B
MSE
158
MET
B
MSE
188
SELENOMETHIONINE
B
MSE
172
MET
B
MSE
205
SELENOMETHIONINE
B
MSE
189
MET
B
MSE
224
SELENOMETHIONINE
B
MSE
208
MET
B
MSE
238
SELENOMETHIONINE
B
MSE
222
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
PHE
83
A
N
PHE
67
A
O
CYS
108
A
O
CYS
92
A
N
ILE
109
A
N
ILE
93
A
O
ILE
141
A
O
ILE
125
A
O
VAL
142
A
O
VAL
126
A
N
LEU
56
A
N
LEU
40
A
N
ALA
53
A
N
ALA
37
A
O
LEU
166
A
O
LEU
150
B
N
PHE
83
B
N
PHE
67
B
O
CYS
108
B
O
CYS
92
B
N
ILE
109
B
N
ILE
93
B
O
SER
143
B
O
SER
127
B
O
VAL
142
B
O
VAL
126
B
N
LEU
56
B
N
LEU
40
B
N
TYR
55
B
N
TYR
39
B
O
TYR
168
B
O
TYR
152
1
A
GLY
0
A
GLY
1
1
Y
1
A
VAL
18
A
VAL
2
1
Y
1
A
HIS
19
A
HIS
3
1
Y
1
A
LEU
20
A
LEU
4
1
Y
1
A
PRO
21
A
PRO
5
1
Y
1
A
ASP
22
A
ASP
6
1
Y
1
A
ASP
23
A
ASP
7
1
Y
1
A
GLU
24
A
GLU
8
1
Y
1
A
THR
25
A
THR
9
1
Y
1
A
PHE
26
A
PHE
10
1
Y
1
A
THR
27
A
THR
11
1
Y
1
A
SER
28
A
SER
12
1
Y
1
A
TYR
29
A
TYR
13
1
Y
1
B
GLY
0
B
GLY
1
1
Y
1
B
VAL
18
B
VAL
2
1
Y
1
B
HIS
19
B
HIS
3
1
Y
1
B
LEU
20
B
LEU
4
1
Y
1
B
PRO
21
B
PRO
5
1
Y
1
B
ASP
22
B
ASP
6
1
Y
1
B
ASP
23
B
ASP
7
1
Y
1
B
GLU
24
B
GLU
8
1
Y
1
B
THR
25
B
THR
9
1
Y
1
B
PHE
26
B
PHE
10
1
Y
1
B
THR
27
B
THR
11
1
Y
1
B
SER
28
B
SER
12
1
Y
1
B
TYR
29
B
TYR
13
1
Y
1
B
TYR
30
B
TYR
14
1
Y
1
A
LEU
87
-67.98
0.22
1
A
ASP
175
-75.95
20.30
1
B
ARG
204
-132.94
-39.51
1
B
ARG
207
86.39
-18.75
199.910
121.4939
86.540
-29.6512
-0.0000
-0.0000
-29.6512
0.0000
-29.6512
1. 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. 2. SULFATE (SO4) MODELED ARE PRESENT IN CRYSTLLIZATION/CRYO CONDITION.
0.2532
0.2237
0.2267
3.0010
46.881
1449
14406
10.0600
99.9000
1.000
0.660
1.1700
1
1.390
SAD
27.6700
0.9000
1.1100
MLHL
FLAT BULK SOLVENT MODEL
83.0410
0.3510
3.0010
46.881
0
3335
25
0
3310
0.002
3393
0.550
4591
0.035
511
0.002
593
14.668
1255
0.3840
0.3310
3.1082
142
1269
1411
10
100.0000
0.3507
0.3226
3.2325
141
1290
1431
10
100.0000
0.3532
0.2986
3.3796
146
1272
1418
10
100.0000
0.3324
0.2832
3.5576
144
1281
1425
10
100.0000
0.2739
0.2403
3.7804
141
1298
1439
10
100.0000
0.2958
0.2251
4.0719
144
1291
1435
10
100.0000
0.2141
0.2084
4.4811
145
1281
1426
10
100.0000
0.2322
0.1843
5.1283
148
1306
1454
10
100.0000
0.2160
0.2096
6.4560
144
1316
1460
10
100.0000
0.1943
0.1799
38.2906
154
1353
1507
10
100.0000
91.955
3.00
46.881
3SC3
14422
-3.000
0.143
1
10.680
99.900
0.014
3.000
3.170
1.6
16285
2175
1
99.900
0.014
3.170
3.280
2.7
8745
1163
1
100.000
0.014
3.280
3.410
3.6
9113
1211
1
100.000
0.014
3.410
3.570
4.9
9140
1222
1
100.000
0.014
3.570
3.760
7.5
9312
1239
1
100.000
0.014
3.760
3.990
9.8
8967
1199
1
100.000
0.014
3.990
4.290
13.1
8984
1200
1
99.900
0.014
4.290
4.720
16.3
9219
1230
1
100.000
0.014
4.720
5.390
18.2
9077
1218
1
100.000
0.014
5.390
6.750
17.7
9191
1246
1
100.000
0.014
6.750
27.2
9314
1324
1
99.400
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
phasing
Eric de La Fortelle
sharp-develop@globalphasing.com
http://www.globalphasing.com/sharp/
SHARP
package
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
December 6, 2007
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.4
data reduction
XDS
phasing
SHELXD
Crystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
A
ASN
35
A
ASN
19
HELX_P
A
SER
47
A
SER
31
1
1
13
A
GLY
63
A
GLY
47
HELX_P
A
LEU
78
A
LEU
62
1
2
16
A
GLY
88
A
GLY
72
HELX_P
A
HIS
90
A
HIS
74
5
3
3
A
SER
94
A
SER
78
HELX_P
A
LEU
98
A
LEU
82
5
4
5
A
GLY
100
A
GLY
84
HELX_P
A
PHE
104
A
PHE
88
5
5
5
A
ASP
111
A
ASP
95
HELX_P
A
ALA
116
A
ALA
100
5
6
6
A
HIS
118
A
HIS
102
HELX_P
A
GLU
134
A
GLU
118
1
7
17
A
LEU
155
A
LEU
139
HELX_P
A
TRP
164
A
TRP
148
1
8
10
A
ASP
176
A
ASP
160
HELX_P
A
ARG
189
A
ARG
173
1
9
14
A
PRO
194
A
PRO
178
HELX_P
A
MSE
205
A
MSE
189
1
10
12
A
ASP
208
A
ASP
192
HELX_P
A
HIS
226
A
HIS
210
1
11
19
A
THR
231
A
THR
215
HELX_P
A
LEU
239
A
LEU
223
1
12
9
B
ASN
35
B
ASN
19
HELX_P
B
ALA
46
B
ALA
30
1
13
12
B
GLY
63
B
GLY
47
HELX_P
B
LEU
78
B
LEU
62
1
14
16
B
GLY
88
B
GLY
72
HELX_P
B
HIS
90
B
HIS
74
5
15
3
B
SER
94
B
SER
78
HELX_P
B
GLU
99
B
GLU
83
5
16
6
B
GLY
100
B
GLY
84
HELX_P
B
PHE
104
B
PHE
88
5
17
5
B
ASP
111
B
ASP
95
HELX_P
B
ALA
116
B
ALA
100
5
18
6
B
HIS
118
B
HIS
102
HELX_P
B
GLN
135
B
GLN
119
1
19
18
B
LEU
155
B
LEU
139
HELX_P
B
TRP
164
B
TRP
148
1
20
10
B
MSE
174
B
MSE
158
HELX_P
B
ARG
189
B
ARG
173
1
21
16
B
PRO
194
B
PRO
178
HELX_P
B
ASN
203
B
ASN
187
1
22
10
B
ASP
208
B
ASP
192
HELX_P
B
GLN
227
B
GLN
211
1
23
20
B
THR
231
B
THR
215
HELX_P
B
LEU
239
B
LEU
223
1
24
9
covale
1.328
both
A
PRO
148
A
C
PRO
132
1_555
A
MSE
149
A
N
MSE
133
1_555
covale
1.326
both
A
MSE
149
A
C
MSE
133
1_555
A
GLU
150
A
N
GLU
134
1_555
covale
1.328
both
A
ARG
161
A
C
ARG
145
1_555
A
MSE
162
A
N
MSE
146
1_555
covale
1.329
both
A
MSE
162
A
C
MSE
146
1_555
A
HIS
163
A
N
HIS
147
1_555
covale
1.326
both
A
PRO
172
A
C
PRO
156
1_555
A
MSE
173
A
N
MSE
157
1_555
covale
1.327
both
A
MSE
173
A
C
MSE
157
1_555
A
MSE
174
A
N
MSE
158
1_555
covale
1.329
both
A
MSE
174
A
C
MSE
158
1_555
A
ASP
175
A
N
ASP
159
1_555
covale
1.329
both
A
ALA
187
A
C
ALA
171
1_555
A
MSE
188
A
N
MSE
172
1_555
covale
1.328
both
A
MSE
188
A
C
MSE
172
1_555
A
ARG
189
A
N
ARG
173
1_555
covale
1.330
both
A
ARG
204
A
C
ARG
188
1_555
A
MSE
205
A
N
MSE
189
1_555
covale
1.329
both
A
MSE
205
A
C
MSE
189
1_555
A
ALA
206
A
N
ALA
190
1_555
covale
1.328
both
A
SER
223
A
C
SER
207
1_555
A
MSE
224
A
N
MSE
208
1_555
covale
1.328
both
A
MSE
224
A
C
MSE
208
1_555
A
VAL
225
A
N
VAL
209
1_555
covale
1.330
both
A
GLU
237
A
C
GLU
221
1_555
A
MSE
238
A
N
MSE
222
1_555
covale
1.329
both
A
MSE
238
A
C
MSE
222
1_555
A
LEU
239
A
N
LEU
223
1_555
covale
1.328
both
B
PRO
148
B
C
PRO
132
1_555
B
MSE
149
B
N
MSE
133
1_555
covale
1.330
both
B
MSE
149
B
C
MSE
133
1_555
B
GLU
150
B
N
GLU
134
1_555
covale
1.329
both
B
ARG
161
B
C
ARG
145
1_555
B
MSE
162
B
N
MSE
146
1_555
covale
1.330
both
B
MSE
162
B
C
MSE
146
1_555
B
HIS
163
B
N
HIS
147
1_555
covale
1.328
both
B
PRO
172
B
C
PRO
156
1_555
B
MSE
173
B
N
MSE
157
1_555
covale
1.328
both
B
MSE
173
B
C
MSE
157
1_555
B
MSE
174
B
N
MSE
158
1_555
covale
1.330
both
B
MSE
174
B
C
MSE
158
1_555
B
ASP
175
B
N
ASP
159
1_555
covale
1.327
both
B
ALA
187
B
C
ALA
171
1_555
B
MSE
188
B
N
MSE
172
1_555
covale
1.328
both
B
MSE
188
B
C
MSE
172
1_555
B
ARG
189
B
N
ARG
173
1_555
covale
1.330
both
B
ARG
204
B
C
ARG
188
1_555
B
MSE
205
B
N
MSE
189
1_555
covale
1.328
both
B
MSE
205
B
C
MSE
189
1_555
B
ALA
206
B
N
ALA
190
1_555
covale
1.329
both
B
SER
223
B
C
SER
207
1_555
B
MSE
224
B
N
MSE
208
1_555
covale
1.328
both
B
MSE
224
B
C
MSE
208
1_555
B
VAL
225
B
N
VAL
209
1_555
covale
1.331
both
B
GLU
237
B
C
GLU
221
1_555
B
MSE
238
B
N
MSE
222
1_555
covale
1.328
both
B
MSE
238
B
C
MSE
222
1_555
B
LEU
239
B
N
LEU
223
1_555
HYDROLASE REGULATOR, DNA BINDING PROTEIN
P-loop containing nucleoside triphosphate hydrolases, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, HYDROLASE, HYDROLASE REGULATOR, DNA BINDING PROTEIN
B
ASP
49
B
ASP
33
1
B
GLY
50
B
GLY
34
0.92
A1S6W5_SHEAM
UNP
1
18
A1S6W5
VHLPDDETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASISTAL
LEGLEQFDLICIDDVDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDE
KLAALQRRAAMRGLQLPEDVGRFLLNRMARDLRTLFDVLDRLDKASMVHQRKLTIPFVKEMLRL
18
241
3SC3
18
241
A1S6W5
A
1
2
225
18
241
3SC3
18
241
A1S6W5
B
1
2
225
1
expression tag
GLY
0
3SC3
A
A1S6W5
UNP
1
2
expression tag
GLY
0
3SC3
B
A1S6W5
UNP
1
5
5
parallel
parallel
parallel
parallel
parallel
parallel
parallel
parallel
A
SER
82
A
SER
66
A
PRO
86
A
PRO
70
A
LEU
106
A
LEU
90
A
ASP
110
A
ASP
94
A
SER
139
A
SER
123
A
ALA
144
A
ALA
128
A
ALA
53
A
ALA
37
A
TRP
57
A
TRP
41
A
LEU
166
A
LEU
150
A
GLN
169
A
GLN
153
B
SER
82
B
SER
66
B
PRO
86
B
PRO
70
B
LEU
106
B
LEU
90
B
ASP
110
B
ASP
94
B
SER
139
B
SER
123
B
ALA
144
B
ALA
128
B
ALA
53
B
ALA
37
B
TRP
57
B
TRP
41
B
TYR
168
B
TYR
152
B
GLN
169
B
GLN
153
BINDING SITE FOR RESIDUE SO4 A 1
A
SO4
1
Software
7
BINDING SITE FOR RESIDUE SO4 A 2
A
SO4
2
Software
5
BINDING SITE FOR RESIDUE SO4 B 3
B
SO4
3
Software
6
BINDING SITE FOR RESIDUE SO4 B 4
B
SO4
4
Software
4
BINDING SITE FOR RESIDUE SO4 B 5
B
SO4
5
Software
4
A
PRO
59
A
PRO
43
7
1_555
A
VAL
60
A
VAL
44
7
1_555
A
LYS
61
A
LYS
45
7
1_555
A
SER
62
A
SER
46
7
1_555
A
GLY
63
A
GLY
47
7
1_555
A
ARG
64
A
ARG
48
7
1_555
A
THR
65
A
THR
49
7
1_555
A
SER
147
A
SER
131
5
1_555
A
PRO
148
A
PRO
132
5
1_555
A
MSE
149
A
MSE
133
5
1_555
A
HIS
163
A
HIS
147
5
1_555
B
LYS
136
B
LYS
120
5
8_656
B
PRO
59
B
PRO
43
6
1_555
B
LYS
61
B
LYS
45
6
1_555
B
SER
62
B
SER
46
6
1_555
B
GLY
63
B
GLY
47
6
1_555
B
ARG
64
B
ARG
48
6
1_555
B
THR
65
B
THR
49
6
1_555
B
SER
147
B
SER
131
4
1_555
B
PRO
148
B
PRO
132
4
1_555
B
MSE
149
B
MSE
133
4
1_555
B
HIS
163
B
HIS
147
4
1_555
B
HIS
90
B
HIS
74
4
1_555
B
ALA
91
B
ALA
75
4
1_555
B
HIS
118
B
HIS
102
4
1_555
B
TRP
121
B
TRP
105
4
1_555
197
I 2 3