0.021345
0.012323
0.000000
0.000000
0.024647
0.000000
0.000000
0.000000
0.010533
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.000
90.000
120.000
46.850
46.850
94.940
C18 H38 O10
414.488
NONAETHYLENE GLYCOL
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
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 uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution
10.2210/pdb3h8u/pdb
pdb_00003h8u
100
1
Adjustable focusing mirrors in K-B geometry
CCD
2008-10-12
MARMOSAIC 300 mm CCD
Si(111) Double Crystal Monochrometer
MAD
M
x-ray
1
0.94645
1.0
0.97965
1.0
23-ID-B
APS
0.94645,0.97965
SYNCHROTRON
APS BEAMLINE 23-ID-B
13458.488
uncharacterized conserved protein with double-stranded beta-helix domain
2
man
polymer
96.063
SULFATE ION
2
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
414.488
NONAETHYLENE GLYCOL
1
syn
non-polymer
18.015
water
207
nat
water
no
yes
G(MSE)GVN(MSE)RAETESRIFSVDEYVRPSNGEPIRSVVLETNDSVVVVWHAHPGQEIASHVHPHGQDTWTVISGEAE
YHQGNGIVTHLKAGDIAIAKPGQVHGA(MSE)NSGPEPFIFVSVVAPGNAGFALAEK
GMGVNMRAETESRIFSVDEYVRPSNGEPIRSVVLETNDSVVVVWHAHPGQEIASHVHPHGQDTWTVISGEAEYHQGNGIV
THLKAGDIAIAKPGQVHGAMNSGPEPFIFVSVVAPGNAGFALAEK
A,B
391713
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
sample
KPN78578_51600, KPN_pKPN5p08243, YP_001338853.1
272620
Klebsiella pneumoniae subsp. pneumoniae MGH 78578
562
Escherichia Coli
HK100
Plasmid
SpeedET
1
2.23
44.96
VAPOR DIFFUSION, SITTING DROP
7.5
1.7000M (NH4)2SO4, 15.0000% Glycerol, 1.7000% PEG-400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
pdbx_struct_assembly_auth_evidence
software
software
struct_conn
database_2
struct_ref_seq_dif
struct_site
repository
Initial release
Advisory
Version format compliance
Author supporting evidence
Refinement description
Data collection
Derived calculations
Refinement description
Database references
Derived calculations
1
0
2009-05-12
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
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2009-04-29
REL
REL
SO4
SULFATE ION
GOL
GLYCEROL
2PE
NONAETHYLENE GLYCOL
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.
SO4
208
2
SO4
SO4
208
A
SO4
209
2
SO4
SO4
209
B
GOL
210
3
GOL
GOL
210
B
2PE
211
4
2PE
2PE
211
B
HOH
125
5
HOH
HOH
125
A
HOH
126
5
HOH
HOH
126
A
HOH
2
5
HOH
HOH
127
A
HOH
128
5
HOH
HOH
128
A
HOH
3
5
HOH
HOH
129
A
HOH
130
5
HOH
HOH
130
A
HOH
5
5
HOH
HOH
131
A
HOH
132
5
HOH
HOH
132
A
HOH
133
5
HOH
HOH
133
A
HOH
7
5
HOH
HOH
134
A
HOH
135
5
HOH
HOH
135
A
HOH
8
5
HOH
HOH
136
A
HOH
11
5
HOH
HOH
137
A
HOH
138
5
HOH
HOH
138
A
HOH
13
5
HOH
HOH
139
A
HOH
140
5
HOH
HOH
140
A
HOH
15
5
HOH
HOH
141
A
HOH
16
5
HOH
HOH
142
A
HOH
17
5
HOH
HOH
143
A
HOH
18
5
HOH
HOH
144
A
HOH
145
5
HOH
HOH
145
A
HOH
146
5
HOH
HOH
146
A
HOH
20
5
HOH
HOH
147
A
HOH
148
5
HOH
HOH
148
A
HOH
149
5
HOH
HOH
149
A
HOH
21
5
HOH
HOH
150
A
HOH
151
5
HOH
HOH
151
A
HOH
152
5
HOH
HOH
152
A
HOH
22
5
HOH
HOH
153
A
HOH
24
5
HOH
HOH
154
A
HOH
26
5
HOH
HOH
155
A
HOH
156
5
HOH
HOH
156
A
HOH
28
5
HOH
HOH
157
A
HOH
158
5
HOH
HOH
158
A
HOH
159
5
HOH
HOH
159
A
HOH
160
5
HOH
HOH
160
A
HOH
161
5
HOH
HOH
161
A
HOH
29
5
HOH
HOH
162
A
HOH
31
5
HOH
HOH
163
A
HOH
164
5
HOH
HOH
164
A
HOH
32
5
HOH
HOH
165
A
HOH
33
5
HOH
HOH
166
A
HOH
167
5
HOH
HOH
167
A
HOH
34
5
HOH
HOH
168
A
HOH
169
5
HOH
HOH
169
A
HOH
35
5
HOH
HOH
170
A
HOH
171
5
HOH
HOH
171
A
HOH
172
5
HOH
HOH
172
A
HOH
36
5
HOH
HOH
173
A
HOH
38
5
HOH
HOH
174
A
HOH
41
5
HOH
HOH
175
A
HOH
176
5
HOH
HOH
176
A
HOH
177
5
HOH
HOH
177
A
HOH
42
5
HOH
HOH
178
A
HOH
43
5
HOH
HOH
179
A
HOH
44
5
HOH
HOH
180
A
HOH
181
5
HOH
HOH
181
A
HOH
45
5
HOH
HOH
182
A
HOH
183
5
HOH
HOH
183
A
HOH
47
5
HOH
HOH
184
A
HOH
185
5
HOH
HOH
185
A
HOH
186
5
HOH
HOH
186
A
HOH
49
5
HOH
HOH
187
A
HOH
188
5
HOH
HOH
188
A
HOH
189
5
HOH
HOH
189
A
HOH
51
5
HOH
HOH
190
A
HOH
191
5
HOH
HOH
191
A
HOH
192
5
HOH
HOH
192
A
HOH
52
5
HOH
HOH
193
A
HOH
54
5
HOH
HOH
194
A
HOH
58
5
HOH
HOH
195
A
HOH
62
5
HOH
HOH
196
A
HOH
197
5
HOH
HOH
197
A
HOH
198
5
HOH
HOH
198
A
HOH
64
5
HOH
HOH
199
A
HOH
200
5
HOH
HOH
200
A
HOH
201
5
HOH
HOH
201
A
HOH
66
5
HOH
HOH
202
A
HOH
70
5
HOH
HOH
203
A
HOH
72
5
HOH
HOH
204
A
HOH
205
5
HOH
HOH
205
A
HOH
73
5
HOH
HOH
206
A
HOH
207
5
HOH
HOH
207
A
HOH
75
5
HOH
HOH
209
A
HOH
76
5
HOH
HOH
210
A
HOH
77
5
HOH
HOH
211
A
HOH
79
5
HOH
HOH
212
A
HOH
80
5
HOH
HOH
213
A
HOH
85
5
HOH
HOH
214
A
HOH
90
5
HOH
HOH
215
A
HOH
93
5
HOH
HOH
216
A
HOH
95
5
HOH
HOH
217
A
HOH
100
5
HOH
HOH
218
A
HOH
101
5
HOH
HOH
219
A
HOH
102
5
HOH
HOH
220
A
HOH
104
5
HOH
HOH
221
A
HOH
107
5
HOH
HOH
222
A
HOH
108
5
HOH
HOH
223
A
HOH
110
5
HOH
HOH
224
A
HOH
112
5
HOH
HOH
225
A
HOH
114
5
HOH
HOH
226
A
HOH
116
5
HOH
HOH
227
A
HOH
120
5
HOH
HOH
228
A
HOH
121
5
HOH
HOH
229
A
HOH
122
5
HOH
HOH
230
A
HOH
147
5
HOH
HOH
231
A
HOH
175
5
HOH
HOH
232
A
HOH
1
5
HOH
HOH
125
B
HOH
4
5
HOH
HOH
126
B
HOH
127
5
HOH
HOH
127
B
HOH
6
5
HOH
HOH
128
B
HOH
129
5
HOH
HOH
129
B
HOH
9
5
HOH
HOH
130
B
HOH
131
5
HOH
HOH
131
B
HOH
10
5
HOH
HOH
132
B
HOH
12
5
HOH
HOH
133
B
HOH
134
5
HOH
HOH
134
B
HOH
14
5
HOH
HOH
135
B
HOH
136
5
HOH
HOH
136
B
HOH
137
5
HOH
HOH
137
B
HOH
19
5
HOH
HOH
138
B
HOH
139
5
HOH
HOH
139
B
HOH
23
5
HOH
HOH
140
B
HOH
141
5
HOH
HOH
141
B
HOH
142
5
HOH
HOH
142
B
HOH
143
5
HOH
HOH
143
B
HOH
144
5
HOH
HOH
144
B
HOH
25
5
HOH
HOH
145
B
HOH
27
5
HOH
HOH
146
B
HOH
30
5
HOH
HOH
148
B
HOH
37
5
HOH
HOH
149
B
HOH
150
5
HOH
HOH
150
B
HOH
39
5
HOH
HOH
151
B
HOH
40
5
HOH
HOH
152
B
HOH
153
5
HOH
HOH
153
B
HOH
154
5
HOH
HOH
154
B
HOH
155
5
HOH
HOH
155
B
HOH
46
5
HOH
HOH
156
B
HOH
157
5
HOH
HOH
157
B
HOH
48
5
HOH
HOH
158
B
HOH
50
5
HOH
HOH
159
B
HOH
53
5
HOH
HOH
160
B
HOH
55
5
HOH
HOH
161
B
HOH
162
5
HOH
HOH
162
B
HOH
163
5
HOH
HOH
163
B
HOH
56
5
HOH
HOH
164
B
HOH
165
5
HOH
HOH
165
B
HOH
166
5
HOH
HOH
166
B
HOH
57
5
HOH
HOH
167
B
HOH
168
5
HOH
HOH
168
B
HOH
59
5
HOH
HOH
169
B
HOH
170
5
HOH
HOH
170
B
HOH
60
5
HOH
HOH
171
B
HOH
61
5
HOH
HOH
172
B
HOH
173
5
HOH
HOH
173
B
HOH
174
5
HOH
HOH
174
B
HOH
63
5
HOH
HOH
176
B
HOH
65
5
HOH
HOH
177
B
HOH
178
5
HOH
HOH
178
B
HOH
179
5
HOH
HOH
179
B
HOH
180
5
HOH
HOH
180
B
HOH
67
5
HOH
HOH
181
B
HOH
182
5
HOH
HOH
182
B
HOH
68
5
HOH
HOH
183
B
HOH
184
5
HOH
HOH
184
B
HOH
69
5
HOH
HOH
185
B
HOH
71
5
HOH
HOH
186
B
HOH
187
5
HOH
HOH
187
B
HOH
74
5
HOH
HOH
188
B
HOH
78
5
HOH
HOH
189
B
HOH
190
5
HOH
HOH
190
B
HOH
81
5
HOH
HOH
191
B
HOH
82
5
HOH
HOH
192
B
HOH
193
5
HOH
HOH
193
B
HOH
194
5
HOH
HOH
194
B
HOH
195
5
HOH
HOH
195
B
HOH
196
5
HOH
HOH
196
B
HOH
83
5
HOH
HOH
197
B
HOH
84
5
HOH
HOH
198
B
HOH
199
5
HOH
HOH
199
B
HOH
86
5
HOH
HOH
200
B
HOH
87
5
HOH
HOH
201
B
HOH
202
5
HOH
HOH
202
B
HOH
203
5
HOH
HOH
203
B
HOH
204
5
HOH
HOH
204
B
HOH
88
5
HOH
HOH
205
B
HOH
206
5
HOH
HOH
206
B
HOH
89
5
HOH
HOH
207
B
HOH
91
5
HOH
HOH
208
B
HOH
92
5
HOH
HOH
212
B
HOH
94
5
HOH
HOH
213
B
HOH
96
5
HOH
HOH
214
B
HOH
97
5
HOH
HOH
215
B
HOH
98
5
HOH
HOH
216
B
HOH
99
5
HOH
HOH
217
B
HOH
103
5
HOH
HOH
218
B
HOH
105
5
HOH
HOH
219
B
HOH
106
5
HOH
HOH
220
B
HOH
109
5
HOH
HOH
221
B
HOH
111
5
HOH
HOH
222
B
HOH
113
5
HOH
HOH
223
B
HOH
115
5
HOH
HOH
224
B
HOH
117
5
HOH
HOH
225
B
HOH
118
5
HOH
HOH
226
B
HOH
119
5
HOH
HOH
227
B
HOH
123
5
HOH
HOH
228
B
HOH
124
5
HOH
HOH
229
B
n
1
0
A
n
2
1
A
n
3
2
A
VAL
3
n
4
VAL
3
A
ASN
4
n
5
ASN
4
A
MSE
5
n
6
MSE
5
A
ARG
6
n
7
ARG
6
A
ALA
7
n
8
ALA
7
A
GLU
8
n
9
GLU
8
A
THR
9
n
10
THR
9
A
GLU
10
n
11
GLU
10
A
SER
11
n
12
SER
11
A
ARG
12
n
13
ARG
12
A
ILE
13
n
14
ILE
13
A
PHE
14
n
15
PHE
14
A
SER
15
n
16
SER
15
A
VAL
16
n
17
VAL
16
A
ASP
17
n
18
ASP
17
A
GLU
18
n
19
GLU
18
A
TYR
19
n
20
TYR
19
A
VAL
20
n
21
VAL
20
A
ARG
21
n
22
ARG
21
A
PRO
22
n
23
PRO
22
A
SER
23
n
24
SER
23
A
ASN
24
n
25
ASN
24
A
GLY
25
n
26
GLY
25
A
GLU
26
n
27
GLU
26
A
PRO
27
n
28
PRO
27
A
ILE
28
n
29
ILE
28
A
ARG
29
n
30
ARG
29
A
SER
30
n
31
SER
30
A
VAL
31
n
32
VAL
31
A
VAL
32
n
33
VAL
32
A
LEU
33
n
34
LEU
33
A
GLU
34
n
35
GLU
34
A
THR
35
n
36
THR
35
A
ASN
36
n
37
ASN
36
A
ASP
37
n
38
ASP
37
A
SER
38
n
39
SER
38
A
VAL
39
n
40
VAL
39
A
VAL
40
n
41
VAL
40
A
VAL
41
n
42
VAL
41
A
VAL
42
n
43
VAL
42
A
TRP
43
n
44
TRP
43
A
HIS
44
n
45
HIS
44
A
ALA
45
n
46
ALA
45
A
HIS
46
n
47
HIS
46
A
PRO
47
n
48
PRO
47
A
GLY
48
n
49
GLY
48
A
GLN
49
n
50
GLN
49
A
GLU
50
n
51
GLU
50
A
ILE
51
n
52
ILE
51
A
ALA
52
n
53
ALA
52
A
SER
53
n
54
SER
53
A
HIS
54
n
55
HIS
54
A
VAL
55
n
56
VAL
55
A
HIS
56
n
57
HIS
56
A
PRO
57
n
58
PRO
57
A
HIS
58
n
59
HIS
58
A
GLY
59
n
60
GLY
59
A
GLN
60
n
61
GLN
60
A
ASP
61
n
62
ASP
61
A
THR
62
n
63
THR
62
A
TRP
63
n
64
TRP
63
A
THR
64
n
65
THR
64
A
VAL
65
n
66
VAL
65
A
ILE
66
n
67
ILE
66
A
SER
67
n
68
SER
67
A
GLY
68
n
69
GLY
68
A
GLU
69
n
70
GLU
69
A
ALA
70
n
71
ALA
70
A
GLU
71
n
72
GLU
71
A
TYR
72
n
73
TYR
72
A
HIS
73
n
74
HIS
73
A
GLN
74
n
75
GLN
74
A
GLY
75
n
76
GLY
75
A
ASN
76
n
77
ASN
76
A
GLY
77
n
78
GLY
77
A
ILE
78
n
79
ILE
78
A
VAL
79
n
80
VAL
79
A
THR
80
n
81
THR
80
A
HIS
81
n
82
HIS
81
A
LEU
82
n
83
LEU
82
A
LYS
83
n
84
LYS
83
A
ALA
84
n
85
ALA
84
A
GLY
85
n
86
GLY
85
A
ASP
86
n
87
ASP
86
A
ILE
87
n
88
ILE
87
A
ALA
88
n
89
ALA
88
A
ILE
89
n
90
ILE
89
A
ALA
90
n
91
ALA
90
A
LYS
91
n
92
LYS
91
A
PRO
92
n
93
PRO
92
A
GLY
93
n
94
GLY
93
A
GLN
94
n
95
GLN
94
A
VAL
95
n
96
VAL
95
A
HIS
96
n
97
HIS
96
A
GLY
97
n
98
GLY
97
A
ALA
98
n
99
ALA
98
A
MSE
99
n
100
MSE
99
A
ASN
100
n
101
ASN
100
A
SER
101
n
102
SER
101
A
GLY
102
n
103
GLY
102
A
PRO
103
n
104
PRO
103
A
GLU
104
n
105
GLU
104
A
PRO
105
n
106
PRO
105
A
PHE
106
n
107
PHE
106
A
ILE
107
n
108
ILE
107
A
PHE
108
n
109
PHE
108
A
VAL
109
n
110
VAL
109
A
SER
110
n
111
SER
110
A
VAL
111
n
112
VAL
111
A
VAL
112
n
113
VAL
112
A
ALA
113
n
114
ALA
113
A
PRO
114
n
115
PRO
114
A
GLY
115
n
116
GLY
115
A
ASN
116
n
117
ASN
116
A
ALA
117
n
118
ALA
117
A
GLY
118
n
119
GLY
118
A
PHE
119
n
120
PHE
119
A
ALA
120
n
121
ALA
120
A
LEU
121
n
122
LEU
121
A
ALA
122
n
123
ALA
122
A
GLU
123
n
124
GLU
123
A
LYS
124
n
125
LYS
124
A
n
1
0
B
n
2
1
B
n
3
2
B
n
4
3
B
n
5
4
B
n
6
5
B
n
7
6
B
n
8
7
B
n
9
8
B
n
10
9
B
GLU
10
n
11
GLU
10
B
SER
11
n
12
SER
11
B
ARG
12
n
13
ARG
12
B
ILE
13
n
14
ILE
13
B
PHE
14
n
15
PHE
14
B
SER
15
n
16
SER
15
B
VAL
16
n
17
VAL
16
B
ASP
17
n
18
ASP
17
B
GLU
18
n
19
GLU
18
B
TYR
19
n
20
TYR
19
B
VAL
20
n
21
VAL
20
B
ARG
21
n
22
ARG
21
B
PRO
22
n
23
PRO
22
B
SER
23
n
24
SER
23
B
ASN
24
n
25
ASN
24
B
GLY
25
n
26
GLY
25
B
GLU
26
n
27
GLU
26
B
PRO
27
n
28
PRO
27
B
ILE
28
n
29
ILE
28
B
ARG
29
n
30
ARG
29
B
SER
30
n
31
SER
30
B
VAL
31
n
32
VAL
31
B
VAL
32
n
33
VAL
32
B
LEU
33
n
34
LEU
33
B
GLU
34
n
35
GLU
34
B
THR
35
n
36
THR
35
B
ASN
36
n
37
ASN
36
B
ASP
37
n
38
ASP
37
B
SER
38
n
39
SER
38
B
VAL
39
n
40
VAL
39
B
VAL
40
n
41
VAL
40
B
VAL
41
n
42
VAL
41
B
VAL
42
n
43
VAL
42
B
TRP
43
n
44
TRP
43
B
HIS
44
n
45
HIS
44
B
ALA
45
n
46
ALA
45
B
HIS
46
n
47
HIS
46
B
PRO
47
n
48
PRO
47
B
GLY
48
n
49
GLY
48
B
GLN
49
n
50
GLN
49
B
GLU
50
n
51
GLU
50
B
ILE
51
n
52
ILE
51
B
ALA
52
n
53
ALA
52
B
SER
53
n
54
SER
53
B
HIS
54
n
55
HIS
54
B
VAL
55
n
56
VAL
55
B
HIS
56
n
57
HIS
56
B
PRO
57
n
58
PRO
57
B
HIS
58
n
59
HIS
58
B
GLY
59
n
60
GLY
59
B
GLN
60
n
61
GLN
60
B
ASP
61
n
62
ASP
61
B
THR
62
n
63
THR
62
B
TRP
63
n
64
TRP
63
B
THR
64
n
65
THR
64
B
VAL
65
n
66
VAL
65
B
ILE
66
n
67
ILE
66
B
SER
67
n
68
SER
67
B
GLY
68
n
69
GLY
68
B
GLU
69
n
70
GLU
69
B
ALA
70
n
71
ALA
70
B
GLU
71
n
72
GLU
71
B
TYR
72
n
73
TYR
72
B
HIS
73
n
74
HIS
73
B
GLN
74
n
75
GLN
74
B
GLY
75
n
76
GLY
75
B
ASN
76
n
77
ASN
76
B
GLY
77
n
78
GLY
77
B
ILE
78
n
79
ILE
78
B
VAL
79
n
80
VAL
79
B
THR
80
n
81
THR
80
B
HIS
81
n
82
HIS
81
B
LEU
82
n
83
LEU
82
B
LYS
83
n
84
LYS
83
B
ALA
84
n
85
ALA
84
B
GLY
85
n
86
GLY
85
B
ASP
86
n
87
ASP
86
B
ILE
87
n
88
ILE
87
B
ALA
88
n
89
ALA
88
B
ILE
89
n
90
ILE
89
B
ALA
90
n
91
ALA
90
B
LYS
91
n
92
LYS
91
B
PRO
92
n
93
PRO
92
B
GLY
93
n
94
GLY
93
B
GLN
94
n
95
GLN
94
B
VAL
95
n
96
VAL
95
B
HIS
96
n
97
HIS
96
B
GLY
97
n
98
GLY
97
B
ALA
98
n
99
ALA
98
B
MSE
99
n
100
MSE
99
B
ASN
100
n
101
ASN
100
B
SER
101
n
102
SER
101
B
GLY
102
n
103
GLY
102
B
PRO
103
n
104
PRO
103
B
GLU
104
n
105
GLU
104
B
PRO
105
n
106
PRO
105
B
PHE
106
n
107
PHE
106
B
ILE
107
n
108
ILE
107
B
PHE
108
n
109
PHE
108
B
VAL
109
n
110
VAL
109
B
SER
110
n
111
SER
110
B
VAL
111
n
112
VAL
111
B
VAL
112
n
113
VAL
112
B
ALA
113
n
114
ALA
113
B
PRO
114
n
115
PRO
114
B
GLY
115
n
116
GLY
115
B
ASN
116
n
117
ASN
116
B
ALA
117
n
118
ALA
117
B
GLY
118
n
119
GLY
118
B
PHE
119
n
120
PHE
119
B
ALA
120
n
121
ALA
120
B
LEU
121
n
122
LEU
121
B
ALA
122
n
123
ALA
122
B
GLU
123
n
124
GLU
123
B
LYS
124
n
125
LYS
124
B
12.7646
-4.3906
0.6205
5.0578
0.5662
2.3682
-0.2143
-0.6326
-0.2985
0.1464
0.0569
0.3094
0.2845
-0.0994
0.1574
-0.1357
-0.0349
-0.0230
-0.1180
0.0465
-0.2014
refined
16.1990
17.5420
27.3090
X-RAY DIFFRACTION
2.2028
-0.2034
-0.3500
0.6139
0.3307
1.9851
-0.0076
-0.0044
-0.0979
-0.0718
-0.0060
-0.0893
0.0025
0.1313
0.0136
-0.2008
-0.0019
0.0006
-0.1857
0.0133
-0.2087
refined
22.6150
19.4710
10.9320
X-RAY DIFFRACTION
12.9662
-6.1159
-5.8857
5.3208
3.1716
5.4456
0.5607
0.0141
0.6840
-0.6237
-0.1407
0.0772
-1.1470
-0.4798
-0.4200
0.0800
0.0702
0.0206
0.0029
0.0149
-0.0761
refined
11.0510
36.3550
9.7540
X-RAY DIFFRACTION
1.2823
-0.4971
-0.7181
1.3451
0.6055
2.2988
0.0635
-0.0739
0.0980
-0.0101
-0.0796
0.0488
-0.1927
-0.0894
0.0162
-0.1939
-0.0176
-0.0008
-0.1472
-0.0053
-0.1988
refined
4.8280
28.6550
19.2960
X-RAY DIFFRACTION
A
3
A
30
X-RAY DIFFRACTION
1
A
31
A
124
X-RAY DIFFRACTION
2
B
11
B
29
X-RAY DIFFRACTION
3
B
30
B
124
X-RAY DIFFRACTION
4
author_and_software_defined_assembly
PISA
2
dimeric
gel filtration
3820
-41
10870
A
MSE
5
SELENOMETHIONINE
A
MSE
6
MET
A
MSE
99
SELENOMETHIONINE
A
MSE
100
MET
B
MSE
99
SELENOMETHIONINE
B
MSE
100
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
14
A
N
PHE
15
B
O
ILE
87
B
O
ILE
88
B
O
ALA
88
B
O
ALA
89
B
N
TRP
63
B
N
TRP
64
B
N
GLN
60
B
N
GLN
61
B
O
ALA
113
B
O
ALA
114
B
O
SER
110
B
O
SER
111
B
N
VAL
41
B
N
VAL
42
B
O
VAL
40
B
O
VAL
41
B
N
LEU
33
B
N
LEU
34
A
N
VAL
32
A
N
VAL
33
A
O
VAL
40
A
O
VAL
41
A
N
VAL
41
A
N
VAL
42
A
O
SER
110
A
O
SER
111
A
O
ALA
113
A
O
ALA
114
A
N
GLN
60
A
N
GLN
61
A
N
TRP
63
A
N
TRP
64
A
O
ALA
88
A
O
ALA
89
A
N
ILE
87
A
N
ILE
88
B
O
PHE
14
B
O
PHE
15
A
O
THR
80
A
O
THR
81
A
N
TYR
72
A
N
TYR
73
A
N
GLU
71
A
N
GLU
72
A
O
MSE
99
A
O
MSE
100
A
O
ALA
98
A
O
ALA
99
A
N
ILE
51
A
N
ILE
52
A
N
VAL
55
A
N
VAL
56
A
O
ALA
120
A
O
ALA
121
B
O
THR
80
B
O
THR
81
B
N
TYR
72
B
N
TYR
73
B
N
GLU
71
B
N
GLU
72
B
O
MSE
99
B
O
MSE
100
B
O
ALA
98
B
O
ALA
99
B
N
ILE
51
B
N
ILE
52
B
N
VAL
55
B
N
VAL
56
B
O
ALA
120
B
O
ALA
121
1
A
CB
VAL
3
A
CB
VAL
4
1
Y
1
A
CG1
VAL
3
A
CG1
VAL
4
1
Y
1
A
CG2
VAL
3
A
CG2
VAL
4
1
Y
1
A
CE
LYS
83
A
CE
LYS
84
1
Y
1
A
NZ
LYS
83
A
NZ
LYS
84
1
Y
1
B
CD
GLU
10
B
CD
GLU
11
1
Y
1
B
OE1
GLU
10
B
OE1
GLU
11
1
Y
1
B
OE2
GLU
10
B
OE2
GLU
11
1
Y
1
B
CG
ASN
24
B
CG
ASN
25
1
Y
1
B
OD1
ASN
24
B
OD1
ASN
25
1
Y
1
B
ND2
ASN
24
B
ND2
ASN
25
1
Y
1
B
CG
GLU
26
B
CG
GLU
27
1
Y
1
B
CD
GLU
26
B
CD
GLU
27
1
Y
1
B
OE1
GLU
26
B
OE1
GLU
27
1
Y
1
B
OE2
GLU
26
B
OE2
GLU
27
1
Y
1
B
C12
2PE
211
F
C12
2PE
1
1
N
1
B
O13
2PE
211
F
O13
2PE
1
1
N
1
B
C14
2PE
211
F
C14
2PE
1
1
N
1
B
C15
2PE
211
F
C15
2PE
1
1
N
1
B
O16
2PE
211
F
O16
2PE
1
1
N
1
B
C17
2PE
211
F
C17
2PE
1
1
N
1
B
C18
2PE
211
F
C18
2PE
1
1
N
1
B
O19
2PE
211
F
O19
2PE
1
1
N
1
B
C20
2PE
211
F
C20
2PE
1
1
N
1
B
C21
2PE
211
F
C21
2PE
1
1
N
1
B
O22
2PE
211
F
O22
2PE
1
1
N
1
B
C23
2PE
211
F
C23
2PE
1
1
N
1
B
C24
2PE
211
F
C24
2PE
1
1
N
1
B
O25
2PE
211
F
O25
2PE
1
1
N
1
B
C26
2PE
211
F
C26
2PE
1
1
N
1
B
C27
2PE
211
F
C27
2PE
1
1
N
1
B
O28
2PE
211
F
O28
2PE
1
1
N
1
A
GLY
0
A
GLY
1
1
Y
1
A
MSE
1
A
MSE
2
1
Y
1
A
GLY
2
A
GLY
3
1
Y
1
B
GLY
0
B
GLY
1
1
Y
1
B
MSE
1
B
MSE
2
1
Y
1
B
GLY
2
B
GLY
3
1
Y
1
B
VAL
3
B
VAL
4
1
Y
1
B
ASN
4
B
ASN
5
1
Y
1
B
MSE
5
B
MSE
6
1
Y
1
B
ARG
6
B
ARG
7
1
Y
1
B
ALA
7
B
ALA
8
1
Y
1
B
GLU
8
B
GLU
9
1
Y
1
B
THR
9
B
THR
10
1
Y
1
A
A
OG
OD1
SER
ASP
15
17
1.91
B
1
B
ASN
116
-117.03
67.71
1
B
ASN
116
-117.03
53.97
71.98
31.881
13.46
0.410
0.210
0.000
0.410
0.000
-0.620
0.970
0.947
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A SULPHATE CATION, GLYCEROL AND PEG FRAGMNET (2PE) MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE.
0.196
0.152
0.154
1.800
24.953
1044
21489
4.900
99.740
1.00
0.50
4.999
0.081
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.115
0.115
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.800
24.953
207
2010
27
0
1776
0.015
0.021
1925
0.002
0.020
1685
1.509
1.924
2645
0.774
3.000
3934
6.733
5.000
258
31.571
24.535
86
11.939
15.000
271
8.859
15.000
7
0.093
0.200
288
0.008
0.020
2223
0.004
0.020
372
0.199
0.200
308
0.181
0.200
1706
0.177
0.200
871
0.082
0.200
1201
0.179
0.200
171
0.127
0.200
8
0.234
0.200
75
0.138
0.200
15
0.756
1.500
1238
0.214
1.500
501
1.214
2.000
1986
1.995
3.000
753
3.213
4.500
650
0.310
0.217
1.848
56
1480
1536
20
98.340
19.864
1.80
24.953
3H8U
21525
-3.00
0.065
1
7.100
2.86
96.600
0.491
1.80
1.86
1.440
5531
3759
1
92.70
0.360
1.86
1.94
2.0
6567
4438
1
95.80
0.234
1.94
2.03
2.9
6285
4251
1
96.40
0.180
2.03
2.13
3.7
5722
3870
1
96.30
0.133
2.13
2.27
4.9
6464
4374
1
96.60
0.104
2.27
2.44
5.8
6019
4088
1
96.90
0.082
2.44
2.69
7.3
6326
4295
1
97.70
0.055
2.69
3.07
10.3
6118
4146
1
98.00
0.040
3.07
3.87
14.5
6273
4258
1
97.70
0.033
3.87
24.953
17.3
6326
4311
1
98.10
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.2.0005
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
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
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
XDS
phasing
SHELXD
phasing
autoSHARP
Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
A
VAL
16
A
VAL
17
HELX_P
A
VAL
20
A
VAL
21
1
1
5
B
VAL
16
B
VAL
17
HELX_P
B
VAL
20
B
VAL
21
1
2
5
covale
1.331
both
A
ASN
4
A
C
ASN
5
1_555
A
MSE
5
A
N
MSE
6
1_555
covale
1.332
both
A
MSE
5
A
C
MSE
6
1_555
A
ARG
6
A
N
ARG
7
1_555
covale
1.338
both
A
ALA
98
A
C
ALA
99
1_555
A
MSE
99
A
N
MSE
100
1_555
covale
1.342
both
A
MSE
99
A
C
MSE
100
1_555
A
ASN
100
A
N
ASN
101
1_555
covale
1.329
both
B
ALA
98
B
C
ALA
99
1_555
B
MSE
99
B
N
MSE
100
1_555
covale
1.337
both
B
MSE
99
B
C
MSE
100
1_555
B
ASN
100
B
N
ASN
101
1_555
structural genomics, unknown function
YP_001338853.1, uncharacterized conserved protein with double-stranded beta-helix domain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Cupin domain, unknown function
A
GLY
102
A
GLY
103
1
A
PRO
103
A
PRO
104
1.92
A
ALA
113
A
ALA
114
1
A
PRO
114
A
PRO
115
-1.78
B
ALA
113
B
ALA
114
1
B
PRO
114
B
PRO
115
1.06
A6TJ50_KLEP7
UNP
1
1
A6TJ50
MGVNMRAETESRIFSVDEYVRPSNGEPIRSVVLETNDSVVVVWHAHPGQEIASHVHPHGQDTWTVISGEAEYHQGNGIVT
HLKAGDIAIAKPGQVHGAMNSGPEPFIFVSVVAPGNAGFALAEK
1
124
3H8U
1
124
A6TJ50
A
1
2
125
1
124
3H8U
1
124
A6TJ50
B
1
2
125
1
expression tag
GLY
0
3H8U
A
A6TJ50
UNP
1
2
expression tag
GLY
0
3H8U
B
A6TJ50
UNP
1
6
6
5
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
13
A
ILE
14
A
SER
15
A
SER
16
B
ASP
86
B
ASP
87
B
ALA
90
B
ALA
91
B
GLN
60
B
GLN
61
B
SER
67
B
SER
68
B
PHE
106
B
PHE
107
B
ALA
113
B
ALA
114
B
VAL
39
B
VAL
40
B
ALA
45
B
ALA
46
B
SER
30
B
SER
31
B
GLU
34
B
GLU
35
A
SER
30
A
SER
31
A
GLU
34
A
GLU
35
A
VAL
39
A
VAL
40
A
ALA
45
A
ALA
46
A
PHE
106
A
PHE
107
A
ALA
113
A
ALA
114
A
GLN
60
A
GLN
61
A
SER
67
A
SER
68
A
ASP
86
A
ASP
87
A
ALA
90
A
ALA
91
B
ILE
13
B
ILE
14
B
SER
15
B
SER
16
A
VAL
79
A
VAL
80
A
LYS
83
A
LYS
84
A
GLU
69
A
GLU
70
A
HIS
73
A
HIS
74
A
HIS
96
A
HIS
97
A
ASN
100
A
ASN
101
A
GLU
50
A
GLU
51
A
VAL
55
A
VAL
56
A
ALA
120
A
ALA
121
A
LEU
121
A
LEU
122
B
VAL
79
B
VAL
80
B
LYS
83
B
LYS
84
B
GLU
69
B
GLU
70
B
HIS
73
B
HIS
74
B
HIS
96
B
HIS
97
B
MSE
99
B
MSE
100
B
GLU
50
B
GLU
51
B
VAL
55
B
VAL
56
B
ALA
120
B
ALA
121
B
LEU
121
B
LEU
122
BINDING SITE FOR RESIDUE SO4 A 208
A
SO4
208
Software
4
BINDING SITE FOR RESIDUE SO4 B 209
B
SO4
209
Software
6
BINDING SITE FOR RESIDUE GOL B 210
B
GOL
210
Software
6
BINDING SITE FOR RESIDUE 2PE B 211
B
2PE
211
Software
6
A
HIS
58
A
HIS
59
4
1_555
A
ALA
117
A
ALA
118
4
1_555
A
GLY
118
A
GLY
119
4
1_555
A
HOH
136
G
HOH
4
1_555
A
ASN
4
A
ASN
5
6
1_555
B
THR
80
B
THR
81
6
1_555
B
HIS
81
B
HIS
82
6
1_555
B
HOH
165
H
HOH
6
1_555
B
HOH
179
H
HOH
6
1_555
B
HOH
202
H
HOH
6
1_555
A
SER
23
A
SER
24
6
2_654
A
ASN
24
A
ASN
25
6
2_654
A
GLY
25
A
GLY
26
6
2_654
A
HOH
172
G
HOH
6
2_654
B
GLU
10
B
GLU
11
6
1_555
B
HOH
129
H
HOH
6
1_555
A
ARG
29
A
ARG
30
6
1_565
A
TRP
43
A
TRP
44
6
1_565
A
ILE
51
A
ILE
52
6
1_565
A
ALA
52
A
ALA
53
6
1_565
A
PHE
119
A
PHE
120
6
1_565
B
ASN
24
B
ASN
25
6
1_555
145
P 32