0.012832
0.007409
0.000000
0.000000
0.014817
0.000000
0.000000
0.000000
0.006885
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
77.930
77.930
145.240
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
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
C4 H10 O3
106.120
DI(HYDROXYETHYL)ETHER
non-polymer
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
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 conserved hypothetical protein (SP_1560) from Streptococcus pneumoniae TIGR4 at 2.74 A resolution
10.2210/pdb4qdy/pdb
pdb_00004qdy
100
1
Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
PIXEL
2013-07-01
DECTRIS PILATUS 6M
single crystal Si(111) bent
MAD
M
x-ray
1
0.91837
1.0
0.97966
1.0
0.97895
1.0
BL11-1
SSRL
0.91837,0.97966,0.97895
SYNCHROTRON
SSRL BEAMLINE BL11-1
24436.973
conserved hypothetical protein
1
man
polymer
106.120
DI(HYDROXYETHYL)ETHER
2
syn
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
12
nat
water
no
yes
GRQVKTETYTNTVTNVPIDIRYNSDKYFISGFASEVSVVLTGANRLSLASE(MSE)QESTRKFKVTADLTDAGVGTIEVP
LSIEDLPNGLTAVATPQKITVKIGKKAQKDKVKIVPEIDPSQIDSRVQIENV(MSE)VSDKEVSITSDQETLDRIDKIIA
VLPTSERITGNYSGSVPLQAIDRNGVVLPAVITPFDTI(MSE)KVTTKPVAPSSSTSNSSTSSSSETSSSTKATSSKTN
GRQVKTETYTNTVTNVPIDIRYNSDKYFISGFASEVSVVLTGANRLSLASEMQESTRKFKVTADLTDAGVGTIEVPLSIE
DLPNGLTAVATPQKITVKIGKKAQKDKVKIVPEIDPSQIDSRVQIENVMVSDKEVSITSDQETLDRIDKIIAVLPTSERI
TGNYSGSVPLQAIDRNGVVLPAVITPFDTIMKVTTKPVAPSSSTSNSSTSSSSETSSSTKATSSKTN
A
JCSG-417515
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
n
n
TIGR4
sample
NP_346007.1, SP_1560
170187
Streptococcus pneumoniae
562
Escherichia Coli
PB1
Plasmid
SpeedET
1
2.60
52.78
VAPOR DIFFUSION, SITTING DROP
42.0% polyethylene glycol 1500, 0.2M ammonium sulfate, 0.1M cesium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Joint Center for Structural Genomics
JCSG
PSI:Biology
software
citation_author
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Structure summary
Refinement description
Database references
Database references
Derived calculations
1
0
2014-07-30
1
1
2014-12-24
1
2
2017-11-22
1
3
2018-01-24
1
4
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
Y
RCSB
Y
RCSB
2014-05-14
REL
REL
PEG
DI(HYDROXYETHYL)ETHER
SO4
SULFATE ION
HOH
water
THE CONSTRUCT (RESIDUES 34-259) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
PEG
260
2
PEG
PEG
301
A
PEG
261
2
PEG
PEG
302
A
SO4
262
3
SO4
SO4
303
A
HOH
263
4
HOH
HOH
401
A
HOH
264
4
HOH
HOH
402
A
HOH
265
4
HOH
HOH
403
A
HOH
266
4
HOH
HOH
404
A
HOH
267
4
HOH
HOH
405
A
HOH
268
4
HOH
HOH
406
A
HOH
269
4
HOH
HOH
407
A
HOH
270
4
HOH
HOH
408
A
HOH
271
4
HOH
HOH
409
A
HOH
272
4
HOH
HOH
410
A
HOH
273
4
HOH
HOH
411
A
HOH
274
4
HOH
HOH
412
A
GLY
0
n
1
GLY
0
A
ARG
34
n
2
ARG
34
A
GLN
35
n
3
GLN
35
A
VAL
36
n
4
VAL
36
A
LYS
37
n
5
LYS
37
A
THR
38
n
6
THR
38
A
GLU
39
n
7
GLU
39
A
THR
40
n
8
THR
40
A
TYR
41
n
9
TYR
41
A
THR
42
n
10
THR
42
A
ASN
43
n
11
ASN
43
A
THR
44
n
12
THR
44
A
VAL
45
n
13
VAL
45
A
THR
46
n
14
THR
46
A
ASN
47
n
15
ASN
47
A
VAL
48
n
16
VAL
48
A
PRO
49
n
17
PRO
49
A
ILE
50
n
18
ILE
50
A
ASP
51
n
19
ASP
51
A
ILE
52
n
20
ILE
52
A
ARG
53
n
21
ARG
53
A
TYR
54
n
22
TYR
54
A
ASN
55
n
23
ASN
55
A
SER
56
n
24
SER
56
A
ASP
57
n
25
ASP
57
A
LYS
58
n
26
LYS
58
A
TYR
59
n
27
TYR
59
A
PHE
60
n
28
PHE
60
A
ILE
61
n
29
ILE
61
A
SER
62
n
30
SER
62
A
GLY
63
n
31
GLY
63
A
PHE
64
n
32
PHE
64
A
ALA
65
n
33
ALA
65
A
SER
66
n
34
SER
66
A
GLU
67
n
35
GLU
67
A
VAL
68
n
36
VAL
68
A
SER
69
n
37
SER
69
A
VAL
70
n
38
VAL
70
A
VAL
71
n
39
VAL
71
A
LEU
72
n
40
LEU
72
A
THR
73
n
41
THR
73
A
GLY
74
n
42
GLY
74
A
ALA
75
n
43
ALA
75
A
ASN
76
n
44
ASN
76
A
ARG
77
n
45
ARG
77
A
LEU
78
n
46
LEU
78
A
SER
79
n
47
SER
79
A
LEU
80
n
48
LEU
80
A
ALA
81
n
49
ALA
81
A
SER
82
n
50
SER
82
A
GLU
83
n
51
GLU
83
A
MSE
84
n
52
MSE
84
A
GLN
85
n
53
GLN
85
A
GLU
86
n
54
GLU
86
A
SER
87
n
55
SER
87
A
THR
88
n
56
THR
88
A
ARG
89
n
57
ARG
89
A
LYS
90
n
58
LYS
90
A
PHE
91
n
59
PHE
91
A
LYS
92
n
60
LYS
92
A
VAL
93
n
61
VAL
93
A
THR
94
n
62
THR
94
A
ALA
95
n
63
ALA
95
A
ASP
96
n
64
ASP
96
A
LEU
97
n
65
LEU
97
A
THR
98
n
66
THR
98
A
ASP
99
n
67
ASP
99
A
ALA
100
n
68
ALA
100
A
GLY
101
n
69
GLY
101
A
VAL
102
n
70
VAL
102
A
GLY
103
n
71
GLY
103
A
THR
104
n
72
THR
104
A
ILE
105
n
73
ILE
105
A
GLU
106
n
74
GLU
106
A
VAL
107
n
75
VAL
107
A
PRO
108
n
76
PRO
108
A
LEU
109
n
77
LEU
109
A
SER
110
n
78
SER
110
A
ILE
111
n
79
ILE
111
A
GLU
112
n
80
GLU
112
A
ASP
113
n
81
ASP
113
A
LEU
114
n
82
LEU
114
A
PRO
115
n
83
PRO
115
A
ASN
116
n
84
ASN
116
A
GLY
117
n
85
GLY
117
A
LEU
118
n
86
LEU
118
A
THR
119
n
87
THR
119
A
ALA
120
n
88
ALA
120
A
VAL
121
n
89
VAL
121
A
ALA
122
n
90
ALA
122
A
THR
123
n
91
THR
123
A
PRO
124
n
92
PRO
124
A
GLN
125
n
93
GLN
125
A
LYS
126
n
94
LYS
126
A
ILE
127
n
95
ILE
127
A
THR
128
n
96
THR
128
A
VAL
129
n
97
VAL
129
A
LYS
130
n
98
LYS
130
A
ILE
131
n
99
ILE
131
A
GLY
132
n
100
GLY
132
A
LYS
133
n
101
LYS
133
A
LYS
134
n
102
LYS
134
A
ALA
135
n
103
ALA
135
A
GLN
136
n
104
GLN
136
A
LYS
137
n
105
LYS
137
A
ASP
138
n
106
ASP
138
A
LYS
139
n
107
LYS
139
A
VAL
140
n
108
VAL
140
A
LYS
141
n
109
LYS
141
A
ILE
142
n
110
ILE
142
A
VAL
143
n
111
VAL
143
A
PRO
144
n
112
PRO
144
A
GLU
145
n
113
GLU
145
A
ILE
146
n
114
ILE
146
A
ASP
147
n
115
ASP
147
A
PRO
148
n
116
PRO
148
A
SER
149
n
117
SER
149
A
GLN
150
n
118
GLN
150
A
ILE
151
n
119
ILE
151
A
ASP
152
n
120
ASP
152
A
SER
153
n
121
SER
153
A
ARG
154
n
122
ARG
154
A
VAL
155
n
123
VAL
155
A
GLN
156
n
124
GLN
156
A
ILE
157
n
125
ILE
157
A
GLU
158
n
126
GLU
158
A
ASN
159
n
127
ASN
159
A
VAL
160
n
128
VAL
160
A
MSE
161
n
129
MSE
161
A
VAL
162
n
130
VAL
162
A
SER
163
n
131
SER
163
A
ASP
164
n
132
ASP
164
A
LYS
165
n
133
LYS
165
A
GLU
166
n
134
GLU
166
A
VAL
167
n
135
VAL
167
A
SER
168
n
136
SER
168
A
ILE
169
n
137
ILE
169
A
THR
170
n
138
THR
170
A
SER
171
n
139
SER
171
A
ASP
172
n
140
ASP
172
A
GLN
173
n
141
GLN
173
A
GLU
174
n
142
GLU
174
A
THR
175
n
143
THR
175
A
LEU
176
n
144
LEU
176
A
ASP
177
n
145
ASP
177
A
ARG
178
n
146
ARG
178
A
ILE
179
n
147
ILE
179
A
ASP
180
n
148
ASP
180
A
LYS
181
n
149
LYS
181
A
ILE
182
n
150
ILE
182
A
ILE
183
n
151
ILE
183
A
ALA
184
n
152
ALA
184
A
VAL
185
n
153
VAL
185
A
LEU
186
n
154
LEU
186
A
PRO
187
n
155
PRO
187
A
THR
188
n
156
THR
188
A
SER
189
n
157
SER
189
A
GLU
190
n
158
GLU
190
A
ARG
191
n
159
ARG
191
A
ILE
192
n
160
ILE
192
A
THR
193
n
161
THR
193
A
GLY
194
n
162
GLY
194
A
ASN
195
n
163
ASN
195
A
TYR
196
n
164
TYR
196
A
SER
197
n
165
SER
197
A
GLY
198
n
166
GLY
198
A
SER
199
n
167
SER
199
A
VAL
200
n
168
VAL
200
A
PRO
201
n
169
PRO
201
A
LEU
202
n
170
LEU
202
A
GLN
203
n
171
GLN
203
A
ALA
204
n
172
ALA
204
A
ILE
205
n
173
ILE
205
A
ASP
206
n
174
ASP
206
A
ARG
207
n
175
ARG
207
A
ASN
208
n
176
ASN
208
A
GLY
209
n
177
GLY
209
A
VAL
210
n
178
VAL
210
A
VAL
211
n
179
VAL
211
A
LEU
212
n
180
LEU
212
A
PRO
213
n
181
PRO
213
A
ALA
214
n
182
ALA
214
A
VAL
215
n
183
VAL
215
A
ILE
216
n
184
ILE
216
A
THR
217
n
185
THR
217
A
PRO
218
n
186
PRO
218
A
PHE
219
n
187
PHE
219
A
ASP
220
n
188
ASP
220
A
THR
221
n
189
THR
221
A
ILE
222
n
190
ILE
222
A
MSE
223
n
191
MSE
223
A
LYS
224
n
192
LYS
224
A
VAL
225
n
193
VAL
225
A
THR
226
n
194
THR
226
A
THR
227
n
195
THR
227
A
LYS
228
n
196
LYS
228
A
PRO
229
n
197
PRO
229
A
VAL
230
n
198
VAL
230
A
n
199
231
A
n
200
232
A
n
201
233
A
n
202
234
A
n
203
235
A
n
204
236
A
n
205
237
A
n
206
238
A
n
207
239
A
n
208
240
A
n
209
241
A
n
210
242
A
n
211
243
A
n
212
244
A
n
213
245
A
n
214
246
A
n
215
247
A
n
216
248
A
n
217
249
A
n
218
250
A
n
219
251
A
n
220
252
A
n
221
253
A
n
222
254
A
n
223
255
A
n
224
256
A
n
225
257
A
n
226
258
A
n
227
259
A
0.4861
0.2692
0.1977
1.7953
-0.8692
1.2657
0.1081
0.0928
-0.0710
-0.0466
-0.0986
0.0079
0.1905
0.0517
-0.0095
0.0700
0.2058
0.0271
-0.1025
-0.0217
-0.0487
refined
36.5669
-2.8805
44.4506
X-RAY DIFFRACTION
A
33
A
230
X-RAY DIFFRACTION
1
{ A|33-230}
author_and_software_defined_assembly
PISA
2
dimeric
3870
-24
20940
A
MSE
84
SELENOMETHIONINE
A
MSE
52
MET
A
MSE
161
SELENOMETHIONINE
A
MSE
129
MET
A
MSE
223
SELENOMETHIONINE
A
MSE
191
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_655
-x+1,-y,z
crystal symmetry operation
77.9300000000
0.0000000000
0.0000000000
A
O
GLU
112
A
O
GLU
80
A
N
LYS
92
A
N
LYS
60
A
O
VAL
93
A
O
VAL
61
A
N
ASP
51
A
N
ASP
19
A
N
VAL
45
A
N
VAL
13
A
O
VAL
70
A
O
VAL
38
A
N
SER
69
A
N
SER
37
A
O
THR
123
A
O
THR
91
A
N
PHE
60
A
N
PHE
28
A
O
GLY
132
A
O
GLY
100
A
O
VAL
129
A
O
VAL
97
A
N
ILE
105
A
N
ILE
73
A
N
PHE
60
A
N
PHE
28
A
O
GLY
132
A
O
GLY
100
A
N
ALA
135
A
N
ALA
103
A
O
SER
171
A
O
SER
139
A
N
THR
170
A
N
THR
138
A
O
VAL
215
A
O
VAL
183
A
N
VAL
143
A
N
VAL
111
A
O
ILE
182
A
O
ILE
150
A
N
ILE
183
A
N
ILE
151
A
O
GLN
203
A
O
GLN
171
A
N
TYR
196
A
N
TYR
164
A
O
VAL
225
A
O
VAL
193
A
O
THR
226
A
O
THR
194
A
N
ASN
159
A
N
ASN
127
1
A
CG
ARG
34
A
CG
ARG
2
1
Y
1
A
CD
ARG
34
A
CD
ARG
2
1
Y
1
A
NE
ARG
34
A
NE
ARG
2
1
Y
1
A
CZ
ARG
34
A
CZ
ARG
2
1
Y
1
A
NH1
ARG
34
A
NH1
ARG
2
1
Y
1
A
NH2
ARG
34
A
NH2
ARG
2
1
Y
1
A
CG
LYS
37
A
CG
LYS
5
1
Y
1
A
CD
LYS
37
A
CD
LYS
5
1
Y
1
A
CE
LYS
37
A
CE
LYS
5
1
Y
1
A
NZ
LYS
37
A
NZ
LYS
5
1
Y
1
A
CG
GLU
39
A
CG
GLU
7
1
Y
1
A
CD
GLU
39
A
CD
GLU
7
1
Y
1
A
OE1
GLU
39
A
OE1
GLU
7
1
Y
1
A
OE2
GLU
39
A
OE2
GLU
7
1
Y
1
A
CG
ASN
43
A
CG
ASN
11
1
Y
1
A
OD1
ASN
43
A
OD1
ASN
11
1
Y
1
A
ND2
ASN
43
A
ND2
ASN
11
1
Y
1
A
CG
LYS
90
A
CG
LYS
58
1
Y
1
A
CD
LYS
90
A
CD
LYS
58
1
Y
1
A
CE
LYS
90
A
CE
LYS
58
1
Y
1
A
NZ
LYS
90
A
NZ
LYS
58
1
Y
1
A
CG
LYS
92
A
CG
LYS
60
1
Y
1
A
CD
LYS
92
A
CD
LYS
60
1
Y
1
A
CE
LYS
92
A
CE
LYS
60
1
Y
1
A
NZ
LYS
92
A
NZ
LYS
60
1
Y
1
A
CG
ASP
99
A
CG
ASP
67
1
Y
1
A
OD1
ASP
99
A
OD1
ASP
67
1
Y
1
A
OD2
ASP
99
A
OD2
ASP
67
1
Y
1
A
CG
LYS
133
A
CG
LYS
101
1
Y
1
A
CD
LYS
133
A
CD
LYS
101
1
Y
1
A
CE
LYS
133
A
CE
LYS
101
1
Y
1
A
NZ
LYS
133
A
NZ
LYS
101
1
Y
1
A
CG
LYS
137
A
CG
LYS
105
1
Y
1
A
CD
LYS
137
A
CD
LYS
105
1
Y
1
A
CE
LYS
137
A
CE
LYS
105
1
Y
1
A
NZ
LYS
137
A
NZ
LYS
105
1
Y
1
A
CG
LYS
141
A
CG
LYS
109
1
Y
1
A
CD
LYS
141
A
CD
LYS
109
1
Y
1
A
CE
LYS
141
A
CE
LYS
109
1
Y
1
A
NZ
LYS
141
A
NZ
LYS
109
1
Y
1
A
CG
ARG
154
A
CG
ARG
122
1
Y
1
A
CD
ARG
154
A
CD
ARG
122
1
Y
1
A
NE
ARG
154
A
NE
ARG
122
1
Y
1
A
CZ
ARG
154
A
CZ
ARG
122
1
Y
1
A
NH1
ARG
154
A
NH1
ARG
122
1
Y
1
A
NH2
ARG
154
A
NH2
ARG
122
1
Y
1
A
CG
GLN
156
A
CG
GLN
124
1
Y
1
A
CD
GLN
156
A
CD
GLN
124
1
Y
1
A
OE1
GLN
156
A
OE1
GLN
124
1
Y
1
A
NE2
GLN
156
A
NE2
GLN
124
1
Y
1
A
CD
LYS
181
A
CD
LYS
149
1
Y
1
A
CE
LYS
181
A
CE
LYS
149
1
Y
1
A
NZ
LYS
181
A
NZ
LYS
149
1
Y
1
A
CG
LYS
224
A
CG
LYS
192
1
Y
1
A
CD
LYS
224
A
CD
LYS
192
1
Y
1
A
CE
LYS
224
A
CE
LYS
192
1
Y
1
A
NZ
LYS
224
A
NZ
LYS
192
1
Y
1
A
CG
LYS
228
A
CG
LYS
196
1
Y
1
A
CD
LYS
228
A
CD
LYS
196
1
Y
1
A
CE
LYS
228
A
CE
LYS
196
1
Y
1
A
NZ
LYS
228
A
NZ
LYS
196
1
Y
1
A
ALA
231
A
ALA
199
1
Y
1
A
PRO
232
A
PRO
200
1
Y
1
A
SER
233
A
SER
201
1
Y
1
A
SER
234
A
SER
202
1
Y
1
A
SER
235
A
SER
203
1
Y
1
A
THR
236
A
THR
204
1
Y
1
A
SER
237
A
SER
205
1
Y
1
A
ASN
238
A
ASN
206
1
Y
1
A
SER
239
A
SER
207
1
Y
1
A
SER
240
A
SER
208
1
Y
1
A
THR
241
A
THR
209
1
Y
1
A
SER
242
A
SER
210
1
Y
1
A
SER
243
A
SER
211
1
Y
1
A
SER
244
A
SER
212
1
Y
1
A
SER
245
A
SER
213
1
Y
1
A
GLU
246
A
GLU
214
1
Y
1
A
THR
247
A
THR
215
1
Y
1
A
SER
248
A
SER
216
1
Y
1
A
SER
249
A
SER
217
1
Y
1
A
SER
250
A
SER
218
1
Y
1
A
THR
251
A
THR
219
1
Y
1
A
LYS
252
A
LYS
220
1
Y
1
A
ALA
253
A
ALA
221
1
Y
1
A
THR
254
A
THR
222
1
Y
1
A
SER
255
A
SER
223
1
Y
1
A
SER
256
A
SER
224
1
Y
1
A
LYS
257
A
LYS
225
1
Y
1
A
THR
258
A
THR
226
1
Y
1
A
ASN
259
A
ASN
227
1
Y
1
A
ARG
34
-93.70
-154.46
1
A
SER
171
-170.20
-167.02
1
A
ALA
184
-103.91
74.72
138.770
65.2071
17.160
-13.3819
0.0000
0.0000
-13.3819
0.0000
26.7639
0.8878
0.8243
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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE EXPERIMENTAL PHASES (MAD) WERE USED AS RESTRAINTS DURING REFINEMENT. 4. POLYETHYLENE GLYCOL FRAGMENTS (PEG) AND SULFATE FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE
0.2878
0.2323
0.2346
2.7400
39.330
342
7370
4.6400
99.9200
1.000
0.500
RANDOM
1
THROUGHOUT
0.000
MAD
0.482
2.7400
39.330
12
1479
19
0
1448
685
SINUSOIDAL
10.000
37
HARMONIC
2.000
211
HARMONIC
5.000
1482
HARMONIC
20.000
228
SEMIHARMONIC
10.000
1658
SEMIHARMONIC
4.000
0.008
1482
HARMONIC
2.000
1.070
2026
HARMONIC
2.000
2.060
1.460
0.2520
0.2695
0.2688
3.0600
84
1936
2020
5
4.1600
99.9200
69.717
2.74
39.330
4QDY
7389
-3.000
0.139
1
18.360
99.700
0.013
2.740
2.840
2.7
9325
727
1
100.000
0.013
2.840
2.950
3.6
8626
691
1
100.000
0.013
2.950
3.080
4.6
7716
693
1
99.600
0.013
3.080
3.250
8.0
9991
745
1
99.600
0.013
3.250
3.450
10.5
9368
704
1
99.700
0.013
3.450
3.710
15.0
9286
721
1
100.000
0.013
3.710
4.080
19.7
9023
729
1
100.000
0.013
4.080
4.670
29.6
8460
753
1
99.900
0.013
4.670
5.860
36.5
9576
767
1
100.000
0.013
5.860
45.7
9177
858
1
98.500
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
refinement
Gerard Bricogne
buster-develop@GlobalPhasing.com
http://www.globalphasing.com/buster/
BUSTER-TNT
program
2.10.0
data reduction
XDS
phasing
SHELXD
refinement
BUSTER
2.10.0
Y
Crystal structure of a YbbR-like protein (SP_1560) from Streptococcus pneumoniae TIGR4 at 2.74 A resolution
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
ASN
76
A
ASN
44
HELX_P
A
GLN
85
A
GLN
53
1
1
10
A
GLN
173
A
GLN
141
HELX_P
A
ARG
178
A
ARG
146
1
2
6
covale
1.343
both
A
GLU
83
A
C
GLU
51
1_555
A
MSE
84
A
N
MSE
52
1_555
covale
1.350
both
A
MSE
84
A
C
MSE
52
1_555
A
GLN
85
A
N
GLN
53
1_555
covale
1.341
both
A
VAL
160
A
C
VAL
128
1_555
A
MSE
161
A
N
MSE
129
1_555
covale
1.339
both
A
MSE
161
A
C
MSE
129
1_555
A
VAL
162
A
N
VAL
130
1_555
covale
1.346
both
A
ILE
222
A
C
ILE
190
1_555
A
MSE
223
A
N
MSE
191
1_555
covale
1.343
both
A
MSE
223
A
C
MSE
191
1_555
A
LYS
224
A
N
LYS
192
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Two YbbR domains, PF07949 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION
A
THR
123
A
THR
91
1
A
PRO
124
A
PRO
92
1.48
A
THR
217
A
THR
185
1
A
PRO
218
A
PRO
186
0.13
Q97PP3_STRPN
UNP
1
34
Q97PP3
RQVKTETYTNTVTNVPIDIRYNSDKYFISGFASEVSVVLTGANRLSLASEMQESTRKFKVTADLTDAGVGTIEVPLSIED
LPNGLTAVATPQKITVKIGKKAQKDKVKIVPEIDPSQIDSRVQIENVMVSDKEVSITSDQETLDRIDKIIAVLPTSERIT
GNYSGSVPLQAIDRNGVVLPAVITPFDTIMKVTTKPVAPSSSTSNSSTSSSSETSSSTKATSSKTN
34
259
4QDY
34
259
Q97PP3
A
1
2
227
1
expression tag
GLY
0
4QDY
A
Q97PP3
UNP
1
5
3
4
5
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
A
SER
110
A
SER
78
A
GLU
112
A
GLU
80
A
LYS
92
A
LYS
60
A
ASP
96
A
ASP
64
A
TYR
41
A
TYR
9
A
ARG
53
A
ARG
21
A
GLU
67
A
GLU
35
A
GLY
74
A
GLY
42
A
THR
119
A
THR
87
A
THR
123
A
THR
91
A
TYR
59
A
TYR
27
A
SER
62
A
SER
30
A
LYS
126
A
LYS
94
A
LYS
139
A
LYS
107
A
GLY
103
A
GLY
71
A
PRO
108
A
PRO
76
A
TYR
59
A
TYR
27
A
SER
62
A
SER
30
A
LYS
126
A
LYS
94
A
LYS
139
A
LYS
107
A
VAL
167
A
VAL
135
A
ASP
172
A
ASP
140
A
VAL
215
A
VAL
183
A
THR
217
A
THR
185
A
ILE
142
A
ILE
110
A
GLU
145
A
GLU
113
A
LYS
181
A
LYS
149
A
VAL
185
A
VAL
153
A
TYR
196
A
TYR
164
A
ILE
205
A
ILE
173
A
ASP
220
A
ASP
188
A
LYS
228
A
LYS
196
A
GLN
156
A
GLN
124
A
VAL
162
A
VAL
130
BINDING SITE FOR RESIDUE PEG A 301
A
PEG
301
Software
6
BINDING SITE FOR RESIDUE PEG A 302
A
PEG
302
Software
3
BINDING SITE FOR RESIDUE SO4 A 303
A
SO4
303
Software
3
A
GLY
63
A
GLY
31
6
1_555
A
PHE
64
A
PHE
32
6
1_555
A
ALA
65
A
ALA
33
6
1_555
A
LEU
212
A
LEU
180
6
4_655
A
PRO
213
A
PRO
181
6
4_655
A
ALA
214
A
ALA
182
6
4_655
A
ASN
55
A
ASN
23
3
1_555
A
LYS
58
A
LYS
26
3
1_555
A
TYR
59
A
TYR
27
3
1_555
A
TYR
41
A
TYR
9
3
1_555
A
ARG
77
A
ARG
45
3
1_555
A
GLU
145
A
GLU
113
3
6_554
181
P 64 2 2