0.015085
0.008709
0.000000
0.000000
0.017419
0.000000
0.000000
0.000000
0.003940
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.000
90.000
120.000
66.290
66.290
253.830
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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 a hypothetical protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution
10.2210/pdb4hyz/pdb
pdb_00004hyz
100
1
Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
PIXEL
2012-06-28
DECTRIS PILATUS 6M
single crystal Si(111) bent
MAD
M
x-ray
1
0.97871
1.0
0.97922
1.0
0.91837
1.0
BL11-1
SSRL
0.97871,0.97922,0.91837
SYNCHROTRON
SSRL BEAMLINE BL11-1
13421.566
Uncharacterized protein
UNP residues 36-148
2
man
polymer
96.063
SULFATE ION
6
syn
non-polymer
35.453
CHLORIDE ION
6
syn
non-polymer
92.094
GLYCEROL
8
syn
non-polymer
18.015
water
107
nat
water
no
yes
GEILKELPEGFDKETVRKQA(MSE)EDIEIAQSKDYESWKSRFTKDLQSSLTEESYDSYLKILEKQGEFKEFGKCTYLGQ
IKDNKKYGGVIIVVKYEEGNVNYSLAYDED(MSE)NLVSFT(MSE)
GEILKELPEGFDKETVRKQAMEDIEIAQSKDYESWKSRFTKDLQSSLTEESYDSYLKILEKQGEFKEFGKCTYLGQIKDN
KKYGGVIIVVKYEEGNVNYSLAYDEDMNLVSFTM
A,B
JCSG-417405
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
sample
29149
411470
Ruminococcus gnavus
562
Escherichia coli
PB1
Plasmid
SpeedET
1
3.00
58.98
VAPOR DIFFUSION, SITTING DROP
4.0
2.40M ammonium sulfate, 0.1M citric acid pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI:Biology
software
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Structure summary
Refinement description
Database references
Derived calculations
1
0
2013-01-09
1
1
2014-12-24
1
2
2017-11-15
1
3
2023-02-01
_software.classification
_software.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
2012-11-14
REL
REL
SO4
SULFATE ION
CL
CHLORIDE ION
GOL
GLYCEROL
HOH
water
THE CONSTRUCT (RESIDUES 37-149) 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
150
2
SO4
SO4
201
A
SO4
152
2
SO4
SO4
202
A
CL
156
3
CL
CL
203
A
CL
159
3
CL
CL
204
A
GOL
162
4
GOL
GOL
205
A
GOL
165
4
GOL
GOL
206
A
GOL
166
4
GOL
GOL
207
A
GOL
168
4
GOL
GOL
208
A
SO4
151
2
SO4
SO4
201
B
SO4
153
2
SO4
SO4
202
B
SO4
154
2
SO4
SO4
203
B
SO4
155
2
SO4
SO4
204
B
CL
157
3
CL
CL
205
B
CL
158
3
CL
CL
206
B
CL
160
3
CL
CL
207
B
CL
161
3
CL
CL
208
B
GOL
163
4
GOL
GOL
209
B
GOL
164
4
GOL
GOL
210
B
GOL
167
4
GOL
GOL
211
B
GOL
169
4
GOL
GOL
212
B
HOH
170
5
HOH
HOH
301
A
HOH
171
5
HOH
HOH
302
A
HOH
172
5
HOH
HOH
303
A
HOH
173
5
HOH
HOH
304
A
HOH
174
5
HOH
HOH
305
A
HOH
175
5
HOH
HOH
306
A
HOH
176
5
HOH
HOH
307
A
HOH
177
5
HOH
HOH
308
A
HOH
178
5
HOH
HOH
309
A
HOH
179
5
HOH
HOH
310
A
HOH
180
5
HOH
HOH
311
A
HOH
181
5
HOH
HOH
312
A
HOH
182
5
HOH
HOH
313
A
HOH
183
5
HOH
HOH
314
A
HOH
184
5
HOH
HOH
315
A
HOH
185
5
HOH
HOH
316
A
HOH
186
5
HOH
HOH
317
A
HOH
187
5
HOH
HOH
318
A
HOH
188
5
HOH
HOH
319
A
HOH
189
5
HOH
HOH
320
A
HOH
190
5
HOH
HOH
321
A
HOH
191
5
HOH
HOH
322
A
HOH
192
5
HOH
HOH
323
A
HOH
193
5
HOH
HOH
324
A
HOH
206
5
HOH
HOH
325
A
HOH
207
5
HOH
HOH
326
A
HOH
208
5
HOH
HOH
327
A
HOH
209
5
HOH
HOH
328
A
HOH
210
5
HOH
HOH
329
A
HOH
211
5
HOH
HOH
330
A
HOH
212
5
HOH
HOH
331
A
HOH
215
5
HOH
HOH
332
A
HOH
216
5
HOH
HOH
333
A
HOH
218
5
HOH
HOH
334
A
HOH
221
5
HOH
HOH
335
A
HOH
222
5
HOH
HOH
336
A
HOH
223
5
HOH
HOH
337
A
HOH
228
5
HOH
HOH
338
A
HOH
229
5
HOH
HOH
339
A
HOH
232
5
HOH
HOH
340
A
HOH
233
5
HOH
HOH
341
A
HOH
234
5
HOH
HOH
342
A
HOH
235
5
HOH
HOH
343
A
HOH
236
5
HOH
HOH
344
A
HOH
237
5
HOH
HOH
345
A
HOH
238
5
HOH
HOH
346
A
HOH
239
5
HOH
HOH
347
A
HOH
240
5
HOH
HOH
348
A
HOH
241
5
HOH
HOH
349
A
HOH
242
5
HOH
HOH
350
A
HOH
243
5
HOH
HOH
351
A
HOH
244
5
HOH
HOH
352
A
HOH
245
5
HOH
HOH
353
A
HOH
246
5
HOH
HOH
354
A
HOH
247
5
HOH
HOH
355
A
HOH
248
5
HOH
HOH
356
A
HOH
249
5
HOH
HOH
357
A
HOH
250
5
HOH
HOH
358
A
HOH
251
5
HOH
HOH
359
A
HOH
252
5
HOH
HOH
360
A
HOH
253
5
HOH
HOH
361
A
HOH
254
5
HOH
HOH
362
A
HOH
255
5
HOH
HOH
363
A
HOH
256
5
HOH
HOH
364
A
HOH
263
5
HOH
HOH
365
A
HOH
265
5
HOH
HOH
366
A
HOH
266
5
HOH
HOH
367
A
HOH
268
5
HOH
HOH
368
A
HOH
194
5
HOH
HOH
301
B
HOH
195
5
HOH
HOH
302
B
HOH
196
5
HOH
HOH
303
B
HOH
197
5
HOH
HOH
304
B
HOH
198
5
HOH
HOH
305
B
HOH
199
5
HOH
HOH
306
B
HOH
200
5
HOH
HOH
307
B
HOH
201
5
HOH
HOH
308
B
HOH
202
5
HOH
HOH
309
B
HOH
203
5
HOH
HOH
310
B
HOH
204
5
HOH
HOH
311
B
HOH
205
5
HOH
HOH
312
B
HOH
213
5
HOH
HOH
313
B
HOH
214
5
HOH
HOH
314
B
HOH
217
5
HOH
HOH
315
B
HOH
219
5
HOH
HOH
316
B
HOH
220
5
HOH
HOH
317
B
HOH
224
5
HOH
HOH
318
B
HOH
225
5
HOH
HOH
319
B
HOH
226
5
HOH
HOH
320
B
HOH
227
5
HOH
HOH
321
B
HOH
230
5
HOH
HOH
322
B
HOH
231
5
HOH
HOH
323
B
HOH
257
5
HOH
HOH
324
B
HOH
258
5
HOH
HOH
325
B
HOH
259
5
HOH
HOH
326
B
HOH
260
5
HOH
HOH
327
B
HOH
261
5
HOH
HOH
328
B
HOH
262
5
HOH
HOH
329
B
HOH
264
5
HOH
HOH
330
B
HOH
267
5
HOH
HOH
331
B
HOH
269
5
HOH
HOH
332
B
HOH
270
5
HOH
HOH
333
B
HOH
271
5
HOH
HOH
334
B
HOH
272
5
HOH
HOH
335
B
HOH
273
5
HOH
HOH
336
B
HOH
274
5
HOH
HOH
337
B
HOH
275
5
HOH
HOH
338
B
HOH
276
5
HOH
HOH
339
B
GLY
0
n
1
GLY
0
A
GLU
37
n
2
GLU
37
A
ILE
38
n
3
ILE
38
A
LEU
39
n
4
LEU
39
A
LYS
40
n
5
LYS
40
A
GLU
41
n
6
GLU
41
A
LEU
42
n
7
LEU
42
A
PRO
43
n
8
PRO
43
A
GLU
44
n
9
GLU
44
A
GLY
45
n
10
GLY
45
A
PHE
46
n
11
PHE
46
A
ASP
47
n
12
ASP
47
A
LYS
48
n
13
LYS
48
A
GLU
49
n
14
GLU
49
A
THR
50
n
15
THR
50
A
VAL
51
n
16
VAL
51
A
ARG
52
n
17
ARG
52
A
LYS
53
n
18
LYS
53
A
GLN
54
n
19
GLN
54
A
ALA
55
n
20
ALA
55
A
MSE
56
n
21
MSE
56
A
GLU
57
n
22
GLU
57
A
ASP
58
n
23
ASP
58
A
ILE
59
n
24
ILE
59
A
GLU
60
n
25
GLU
60
A
ILE
61
n
26
ILE
61
A
ALA
62
n
27
ALA
62
A
GLN
63
n
28
GLN
63
A
SER
64
n
29
SER
64
A
LYS
65
n
30
LYS
65
A
ASP
66
n
31
ASP
66
A
TYR
67
n
32
TYR
67
A
GLU
68
n
33
GLU
68
A
SER
69
n
34
SER
69
A
TRP
70
n
35
TRP
70
A
LYS
71
n
36
LYS
71
A
SER
72
n
37
SER
72
A
ARG
73
n
38
ARG
73
A
PHE
74
n
39
PHE
74
A
THR
75
n
40
THR
75
A
LYS
76
n
41
LYS
76
A
ASP
77
n
42
ASP
77
A
LEU
78
n
43
LEU
78
A
GLN
79
n
44
GLN
79
A
SER
80
n
45
SER
80
A
SER
81
n
46
SER
81
A
LEU
82
n
47
LEU
82
A
THR
83
n
48
THR
83
A
GLU
84
n
49
GLU
84
A
GLU
85
n
50
GLU
85
A
SER
86
n
51
SER
86
A
TYR
87
n
52
TYR
87
A
ASP
88
n
53
ASP
88
A
SER
89
n
54
SER
89
A
TYR
90
n
55
TYR
90
A
LEU
91
n
56
LEU
91
A
LYS
92
n
57
LYS
92
A
ILE
93
n
58
ILE
93
A
LEU
94
n
59
LEU
94
A
GLU
95
n
60
GLU
95
A
LYS
96
n
61
LYS
96
A
GLN
97
n
62
GLN
97
A
GLY
98
n
63
GLY
98
A
GLU
99
n
64
GLU
99
A
PHE
100
n
65
PHE
100
A
LYS
101
n
66
LYS
101
A
GLU
102
n
67
GLU
102
A
PHE
103
n
68
PHE
103
A
GLY
104
n
69
GLY
104
A
LYS
105
n
70
LYS
105
A
CYS
106
n
71
CYS
106
A
THR
107
n
72
THR
107
A
TYR
108
n
73
TYR
108
A
LEU
109
n
74
LEU
109
A
GLY
110
n
75
GLY
110
A
GLN
111
n
76
GLN
111
A
ILE
112
n
77
ILE
112
A
LYS
113
n
78
LYS
113
A
ASP
114
n
79
ASP
114
A
ASN
115
n
80
ASN
115
A
LYS
116
n
81
LYS
116
A
LYS
117
n
82
LYS
117
A
TYR
118
n
83
TYR
118
A
GLY
119
n
84
GLY
119
A
GLY
120
n
85
GLY
120
A
VAL
121
n
86
VAL
121
A
ILE
122
n
87
ILE
122
A
ILE
123
n
88
ILE
123
A
VAL
124
n
89
VAL
124
A
VAL
125
n
90
VAL
125
A
LYS
126
n
91
LYS
126
A
TYR
127
n
92
TYR
127
A
GLU
128
n
93
GLU
128
A
GLU
129
n
94
GLU
129
A
GLY
130
n
95
GLY
130
A
ASN
131
n
96
ASN
131
A
VAL
132
n
97
VAL
132
A
ASN
133
n
98
ASN
133
A
TYR
134
n
99
TYR
134
A
SER
135
n
100
SER
135
A
LEU
136
n
101
LEU
136
A
ALA
137
n
102
ALA
137
A
TYR
138
n
103
TYR
138
A
ASP
139
n
104
ASP
139
A
GLU
140
n
105
GLU
140
A
ASP
141
n
106
ASP
141
A
MSE
142
n
107
MSE
142
A
ASN
143
n
108
ASN
143
A
LEU
144
n
109
LEU
144
A
VAL
145
n
110
VAL
145
A
SER
146
n
111
SER
146
A
PHE
147
n
112
PHE
147
A
THR
148
n
113
THR
148
A
MSE
149
n
114
MSE
149
A
GLY
0
n
1
GLY
0
B
GLU
37
n
2
GLU
37
B
ILE
38
n
3
ILE
38
B
LEU
39
n
4
LEU
39
B
LYS
40
n
5
LYS
40
B
GLU
41
n
6
GLU
41
B
LEU
42
n
7
LEU
42
B
PRO
43
n
8
PRO
43
B
GLU
44
n
9
GLU
44
B
GLY
45
n
10
GLY
45
B
PHE
46
n
11
PHE
46
B
ASP
47
n
12
ASP
47
B
LYS
48
n
13
LYS
48
B
GLU
49
n
14
GLU
49
B
THR
50
n
15
THR
50
B
VAL
51
n
16
VAL
51
B
ARG
52
n
17
ARG
52
B
LYS
53
n
18
LYS
53
B
GLN
54
n
19
GLN
54
B
ALA
55
n
20
ALA
55
B
MSE
56
n
21
MSE
56
B
GLU
57
n
22
GLU
57
B
ASP
58
n
23
ASP
58
B
ILE
59
n
24
ILE
59
B
GLU
60
n
25
GLU
60
B
ILE
61
n
26
ILE
61
B
ALA
62
n
27
ALA
62
B
GLN
63
n
28
GLN
63
B
SER
64
n
29
SER
64
B
LYS
65
n
30
LYS
65
B
ASP
66
n
31
ASP
66
B
TYR
67
n
32
TYR
67
B
GLU
68
n
33
GLU
68
B
SER
69
n
34
SER
69
B
TRP
70
n
35
TRP
70
B
LYS
71
n
36
LYS
71
B
SER
72
n
37
SER
72
B
ARG
73
n
38
ARG
73
B
PHE
74
n
39
PHE
74
B
THR
75
n
40
THR
75
B
LYS
76
n
41
LYS
76
B
ASP
77
n
42
ASP
77
B
LEU
78
n
43
LEU
78
B
GLN
79
n
44
GLN
79
B
SER
80
n
45
SER
80
B
SER
81
n
46
SER
81
B
LEU
82
n
47
LEU
82
B
THR
83
n
48
THR
83
B
GLU
84
n
49
GLU
84
B
GLU
85
n
50
GLU
85
B
SER
86
n
51
SER
86
B
TYR
87
n
52
TYR
87
B
ASP
88
n
53
ASP
88
B
SER
89
n
54
SER
89
B
TYR
90
n
55
TYR
90
B
LEU
91
n
56
LEU
91
B
LYS
92
n
57
LYS
92
B
ILE
93
n
58
ILE
93
B
LEU
94
n
59
LEU
94
B
GLU
95
n
60
GLU
95
B
LYS
96
n
61
LYS
96
B
GLN
97
n
62
GLN
97
B
GLY
98
n
63
GLY
98
B
GLU
99
n
64
GLU
99
B
PHE
100
n
65
PHE
100
B
LYS
101
n
66
LYS
101
B
GLU
102
n
67
GLU
102
B
PHE
103
n
68
PHE
103
B
GLY
104
n
69
GLY
104
B
LYS
105
n
70
LYS
105
B
CYS
106
n
71
CYS
106
B
THR
107
n
72
THR
107
B
TYR
108
n
73
TYR
108
B
LEU
109
n
74
LEU
109
B
GLY
110
n
75
GLY
110
B
GLN
111
n
76
GLN
111
B
ILE
112
n
77
ILE
112
B
LYS
113
n
78
LYS
113
B
ASP
114
n
79
ASP
114
B
ASN
115
n
80
ASN
115
B
LYS
116
n
81
LYS
116
B
LYS
117
n
82
LYS
117
B
TYR
118
n
83
TYR
118
B
GLY
119
n
84
GLY
119
B
GLY
120
n
85
GLY
120
B
VAL
121
n
86
VAL
121
B
ILE
122
n
87
ILE
122
B
ILE
123
n
88
ILE
123
B
VAL
124
n
89
VAL
124
B
VAL
125
n
90
VAL
125
B
LYS
126
n
91
LYS
126
B
TYR
127
n
92
TYR
127
B
GLU
128
n
93
GLU
128
B
GLU
129
n
94
GLU
129
B
GLY
130
n
95
GLY
130
B
ASN
131
n
96
ASN
131
B
VAL
132
n
97
VAL
132
B
ASN
133
n
98
ASN
133
B
TYR
134
n
99
TYR
134
B
SER
135
n
100
SER
135
B
LEU
136
n
101
LEU
136
B
ALA
137
n
102
ALA
137
B
TYR
138
n
103
TYR
138
B
ASP
139
n
104
ASP
139
B
GLU
140
n
105
GLU
140
B
ASP
141
n
106
ASP
141
B
MSE
142
n
107
MSE
142
B
ASN
143
n
108
ASN
143
B
LEU
144
n
109
LEU
144
B
VAL
145
n
110
VAL
145
B
SER
146
n
111
SER
146
B
PHE
147
n
112
PHE
147
B
THR
148
n
113
THR
148
B
MSE
149
n
114
MSE
149
B
2.9009
-1.2283
-1.5242
3.5409
2.2114
3.8883
-0.1701
-0.0365
-0.1488
0.3365
0.0488
-0.2847
0.5794
0.2149
0.1213
0.0107
0.0088
0.0560
-0.0947
0.0145
-0.1027
refined
54.1434
-30.5441
136.9410
X-RAY DIFFRACTION
2.8011
-0.2438
1.6201
2.7052
0.9042
4.7257
-0.1918
-0.1888
0.3194
-0.1948
-0.2601
0.3419
-0.6217
-0.3797
0.4520
-0.0363
0.0244
-0.1281
-0.1575
-0.1188
0.0272
refined
21.6714
-19.1341
138.9340
X-RAY DIFFRACTION
A
0
A
149
X-RAY DIFFRACTION
1
B
0
B
149
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
4
tetrameric
10850
-311
23540
A
MSE
56
SELENOMETHIONINE
A
MSE
21
MET
A
MSE
142
SELENOMETHIONINE
A
MSE
107
MET
A
MSE
149
SELENOMETHIONINE
A
MSE
114
MET
B
MSE
56
SELENOMETHIONINE
B
MSE
21
MET
B
MSE
142
SELENOMETHIONINE
B
MSE
107
MET
B
MSE
149
SELENOMETHIONINE
B
MSE
114
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
0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
10_556
-y,-x,-z+7/6
crystal symmetry operation
0.0000000000
0.0000000000
296.1350000000
A
N
LEU
39
A
N
LEU
4
A
O
GLY
110
A
O
GLY
75
A
N
GLU
102
A
N
GLU
67
A
O
LYS
126
A
O
LYS
91
A
N
VAL
125
A
N
VAL
90
A
O
VAL
132
A
O
VAL
97
A
N
SER
135
A
N
SER
100
A
O
THR
148
A
O
THR
113
B
N
LEU
39
B
N
LEU
4
B
O
GLY
110
B
O
GLY
75
B
N
GLY
104
B
N
GLY
69
B
O
VAL
124
B
O
VAL
89
B
N
VAL
125
B
N
VAL
90
B
O
VAL
132
B
O
VAL
97
B
N
SER
135
B
N
SER
100
B
O
THR
148
B
O
THR
113
1
A
CG
GLU
44
A
CG
GLU
9
1
Y
1
A
CD
GLU
44
A
CD
GLU
9
1
Y
1
A
OE1
GLU
44
A
OE1
GLU
9
1
Y
1
A
OE2
GLU
44
A
OE2
GLU
9
1
Y
1
A
CG
GLU
85
A
CG
GLU
50
1
Y
1
A
CD
GLU
85
A
CD
GLU
50
1
Y
1
A
OE1
GLU
85
A
OE1
GLU
50
1
Y
1
A
OE2
GLU
85
A
OE2
GLU
50
1
Y
1
A
CD
LYS
92
A
CD
LYS
57
1
Y
1
A
CE
LYS
92
A
CE
LYS
57
1
Y
1
A
NZ
LYS
92
A
NZ
LYS
57
1
Y
1
A
CE
LYS
101
A
CE
LYS
66
1
Y
1
A
NZ
LYS
101
A
NZ
LYS
66
1
Y
1
A
CE
LYS
105
A
CE
LYS
70
1
Y
1
A
NZ
LYS
105
A
NZ
LYS
70
1
Y
1
A
CE
LYS
116
A
CE
LYS
81
1
Y
1
A
NZ
LYS
116
A
NZ
LYS
81
1
Y
1
A
CD
GLU
128
A
CD
GLU
93
1
Y
1
A
OE1
GLU
128
A
OE1
GLU
93
1
Y
1
A
OE2
GLU
128
A
OE2
GLU
93
1
Y
1
B
CD
GLU
44
B
CD
GLU
9
1
Y
1
B
OE1
GLU
44
B
OE1
GLU
9
1
Y
1
B
OE2
GLU
44
B
OE2
GLU
9
1
Y
1
B
CG
GLU
85
B
CG
GLU
50
1
Y
1
B
CD
GLU
85
B
CD
GLU
50
1
Y
1
B
OE1
GLU
85
B
OE1
GLU
50
1
Y
1
B
OE2
GLU
85
B
OE2
GLU
50
1
Y
1
B
CE
LYS
92
B
CE
LYS
57
1
Y
1
B
NZ
LYS
92
B
NZ
LYS
57
1
Y
1
B
CG
GLU
95
B
CG
GLU
60
1
Y
1
B
CD
GLU
95
B
CD
GLU
60
1
Y
1
B
OE1
GLU
95
B
OE1
GLU
60
1
Y
1
B
OE2
GLU
95
B
OE2
GLU
60
1
Y
1
B
CD
LYS
101
B
CD
LYS
66
1
Y
1
B
CE
LYS
101
B
CE
LYS
66
1
Y
1
B
NZ
LYS
101
B
NZ
LYS
66
1
Y
1
B
CE
LYS
113
B
CE
LYS
78
1
Y
1
B
NZ
LYS
113
B
NZ
LYS
78
1
Y
1
B
CE
LYS
116
B
CE
LYS
81
1
Y
1
B
NZ
LYS
116
B
NZ
LYS
81
1
Y
1
B
CG
GLU
128
B
CG
GLU
93
1
Y
1
B
CD
GLU
128
B
CD
GLU
93
1
Y
1
B
OE1
GLU
128
B
OE1
GLU
93
1
Y
1
B
OE2
GLU
128
B
OE2
GLU
93
1
Y
1
A
LYS
40
-98.31
32.17
1
B
LYS
40
-97.50
34.14
132.060
51.5237
21.130
-1.6180
0.0000
0.0000
-1.6180
0.0000
3.2360
0.9447
0.9364
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 MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4.SULFATE (SO4) FROM THE CRYSTALLIZATION, GLYCEROL(GOL), USED AS A CRYOPROTECTANT, AND CHLORIDE FROM THE PURIFICATION BUFFER HAVE BEEN MODELED INTO THE STRUCTURE. 5. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.UNEXPLAINED DIFFERENCE DENSITY NEAR TYR 118 ON THE A AND B SUBUNITS WAS NOT MODELED.
0.2084
0.1865
0.1876
2.2500
29.377
842
16601
5.0700
99.9600
1.000
0.500
RANDOM
1
THROUGHOUT
0.000
MAD
0.315
2.2500
29.377
107
2013
84
0
1822
914
SINUSOIDAL
2.000
59
HARMONIC
2.000
265
HARMONIC
5.000
1935
HARMONIC
20.000
239
SEMIHARMONIC
5.000
2198
SEMIHARMONIC
4.000
0.010
1935
HARMONIC
2.000
1.060
2593
HARMONIC
2.000
3.740
2.800
0.2277
0.1977
0.1992
2.4000
152
2757
2909
8
5.2300
99.9600
43.423
2.25
29.377
4HYZ
16696
16696
0.103
1
15.000
11.100
99.900
0.873
2.250
2.310
0.9
11870
1191
0.873
1
10.000
100.000
0.729
2.310
2.370
1.1
13496
1175
0.729
1
11.500
100.000
0.605
2.370
2.440
1.3
13611
1112
0.605
1
12.200
100.000
0.536
2.440
2.520
1.4
13256
1106
0.536
1
12.000
100.000
0.436
2.520
2.600
1.8
12372
1068
0.436
1
11.600
100.000
0.363
2.600
2.690
2.1
11606
1028
0.363
1
11.300
100.000
0.268
2.690
2.790
2.9
10420
1025
0.268
1
10.200
100.000
0.198
2.790
2.900
3.8
10487
968
0.198
1
10.800
100.000
0.171
2.900
3.030
4.4
11395
954
0.171
1
11.900
100.000
0.135
3.030
3.180
5.6
10594
889
0.135
1
11.900
100.000
0.105
3.180
3.350
6.9
9971
863
0.105
1
11.600
100.000
0.085
3.350
3.560
8.2
9027
804
0.085
1
11.200
100.000
0.065
3.560
3.800
10.7
7804
787
0.065
1
9.900
100.000
0.060
3.800
4.110
11.5
8837
733
0.060
1
12.100
100.000
0.053
4.110
4.500
12.8
7702
670
0.053
1
11.500
100.000
0.051
4.500
5.030
13.2
6819
624
0.051
1
10.900
100.000
0.059
5.030
5.810
11.5
5179
561
0.059
1
9.200
100.000
0.073
5.810
7.120
9.4
5498
490
0.073
1
11.200
100.000
0.046
7.120
10.060
14.5
3737
392
0.046
1
9.500
99.900
0.040
10.060
29.377
16.0
2190
256
0.040
1
8.600
96.300
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
Phil Evans
pre@mrc-lmb.cam.ac.uk
SCALA
package
3.3.20
refinement
Gerard Bricogne
buster-develop@GlobalPhasing.com
http://www.globalphasing.com/buster/
BUSTER-TNT
program
2.10.0
data reduction
MOSFLM
phasing
SHELXD
refinement
BUSTER
2.10.0
Y
Crystal structure of a DUF3887 family protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
5
N
N
5
N
N
A
ASP
47
A
ASP
12
HELX_P
A
SER
64
A
SER
29
1
1
18
A
ASP
66
A
ASP
31
HELX_P
A
SER
72
A
SER
37
1
2
7
A
THR
75
A
THR
40
HELX_P
A
SER
80
A
SER
45
1
3
6
A
THR
83
A
THR
48
HELX_P
A
LYS
96
A
LYS
61
1
4
14
B
ASP
47
B
ASP
12
HELX_P
B
SER
64
B
SER
29
1
5
18
B
ASP
66
B
ASP
31
HELX_P
B
SER
72
B
SER
37
1
6
7
B
THR
75
B
THR
40
HELX_P
B
SER
80
B
SER
45
1
7
6
B
THR
83
B
THR
48
HELX_P
B
LYS
96
B
LYS
61
1
8
14
covale
1.337
both
A
ALA
55
A
C
ALA
20
1_555
A
MSE
56
A
N
MSE
21
1_555
covale
1.340
both
A
MSE
56
A
C
MSE
21
1_555
A
GLU
57
A
N
GLU
22
1_555
covale
1.349
both
A
ASP
141
A
C
ASP
106
1_555
A
MSE
142
A
N
MSE
107
1_555
covale
1.341
both
A
MSE
142
A
C
MSE
107
1_555
A
ASN
143
A
N
ASN
108
1_555
covale
1.322
both
A
THR
148
A
C
THR
113
1_555
A
MSE
149
A
N
MSE
114
1_555
covale
1.328
both
B
ALA
55
B
C
ALA
20
1_555
B
MSE
56
B
N
MSE
21
1_555
covale
1.342
both
B
MSE
56
B
C
MSE
21
1_555
B
GLU
57
B
N
GLU
22
1_555
covale
1.341
both
B
ASP
141
B
C
ASP
106
1_555
B
MSE
142
B
N
MSE
107
1_555
covale
1.348
both
B
MSE
142
B
C
MSE
107
1_555
B
ASN
143
B
N
ASN
108
1_555
covale
1.322
both
B
THR
148
B
C
THR
113
1_555
B
MSE
149
B
N
MSE
114
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
PF13026 family protein, DUF3887, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION
A7B2S7_RUMGN
UNP
1
37
A7B2S7
EILKELPEGFDKETVRKQAMEDIEIAQSKDYESWKSRFTKDLQSSLTEESYDSYLKILEKQGEFKEFGKCTYLGQIKDNK
KYGGVIIVVKYEEGNVNYSLAYDEDMNLVSFTM
37
149
4HYZ
37
149
A7B2S7
A
1
2
114
37
149
4HYZ
37
149
A7B2S7
B
1
2
114
1
expression tag
GLY
0
4HYZ
A
A7B2S7
UNP
1
2
expression tag
GLY
0
4HYZ
B
A7B2S7
UNP
1
5
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLU
37
A
GLU
2
A
LEU
39
A
LEU
4
A
PHE
100
A
PHE
65
A
LYS
113
A
LYS
78
A
LYS
116
A
LYS
81
A
TYR
127
A
TYR
92
A
GLY
130
A
GLY
95
A
TYR
138
A
TYR
103
A
LEU
144
A
LEU
109
A
THR
148
A
THR
113
B
GLU
37
B
GLU
2
B
LEU
39
B
LEU
4
B
PHE
100
B
PHE
65
B
LYS
113
B
LYS
78
B
LYS
116
B
LYS
81
B
TYR
127
B
TYR
92
B
GLY
130
B
GLY
95
B
TYR
138
B
TYR
103
B
LEU
144
B
LEU
109
B
THR
148
B
THR
113
BINDING SITE FOR RESIDUE SO4 A 201
A
SO4
201
Software
7
BINDING SITE FOR RESIDUE SO4 A 202
A
SO4
202
Software
6
BINDING SITE FOR RESIDUE CL A 203
A
CL
203
Software
1
BINDING SITE FOR RESIDUE CL A 204
A
CL
204
Software
2
BINDING SITE FOR RESIDUE GOL A 205
A
GOL
205
Software
4
BINDING SITE FOR RESIDUE GOL A 206
A
GOL
206
Software
4
BINDING SITE FOR RESIDUE GOL A 207
A
GOL
207
Software
4
BINDING SITE FOR RESIDUE GOL A 208
A
GOL
208
Software
4
BINDING SITE FOR RESIDUE SO4 B 201
B
SO4
201
Software
5
BINDING SITE FOR RESIDUE SO4 B 202
B
SO4
202
Software
6
BINDING SITE FOR RESIDUE SO4 B 203
B
SO4
203
Software
5
BINDING SITE FOR RESIDUE SO4 B 204
B
SO4
204
Software
5
BINDING SITE FOR RESIDUE CL B 205
B
CL
205
Software
1
BINDING SITE FOR RESIDUE CL B 206
B
CL
206
Software
2
BINDING SITE FOR RESIDUE CL B 207
B
CL
207
Software
3
BINDING SITE FOR RESIDUE CL B 208
B
CL
208
Software
1
BINDING SITE FOR RESIDUE GOL B 209
B
GOL
209
Software
3
BINDING SITE FOR RESIDUE GOL B 210
B
GOL
210
Software
3
BINDING SITE FOR RESIDUE GOL B 211
B
GOL
211
Software
1
BINDING SITE FOR RESIDUE GOL B 212
B
GOL
212
Software
7
A
GLY
0
A
GLY
1
7
1_555
A
LYS
113
A
LYS
78
7
1_555
A
ASP
114
A
ASP
79
7
1_555
A
ASN
131
A
ASN
96
7
10_556
A
HOH
322
W
HOH
7
1_555
A
HOH
323
W
HOH
7
10_556
A
HOH
363
W
HOH
7
1_555
A
THR
75
A
THR
40
6
1_555
A
LYS
76
A
LYS
41
6
1_555
A
ASP
139
A
ASP
104
6
1_555
A
ASP
141
A
ASP
106
6
1_555
A
ASN
143
A
ASN
108
6
1_555
A
HOH
361
W
HOH
6
1_555
A
GLY
45
A
GLY
10
1
1_555
A
LYS
48
A
LYS
13
2
1_555
A
HOH
329
W
HOH
2
1_555
A
LYS
116
A
LYS
81
4
1_555
A
LYS
117
A
LYS
82
4
1_555
A
GLU
140
A
GLU
105
4
1_555
A
HOH
316
W
HOH
4
1_555
A
GLU
57
A
GLU
22
4
1_555
A
GLU
60
A
GLU
25
4
1_555
B
ILE
61
B
ILE
26
4
8_546
B
HOH
308
X
HOH
4
8_546
A
ARG
52
A
ARG
17
4
1_555
A
CYS
106
A
CYS
71
4
1_555
A
TYR
108
A
TYR
73
4
1_555
B
CL
206
P
CL
4
1_555
A
LEU
82
A
LEU
47
4
1_555
A
THR
83
A
THR
48
4
1_555
A
GLU
84
A
GLU
49
4
1_555
B
LYS
76
B
LYS
41
4
1_655
A
LYS
40
A
LYS
5
5
10_556
A
LYS
48
A
LYS
13
5
1_555
B
LYS
40
B
LYS
5
5
10_556
B
LYS
48
B
LYS
13
5
1_555
B
HOH
311
X
HOH
5
10_556
B
GLY
0
B
GLY
1
6
1_555
B
LYS
113
B
LYS
78
6
1_555
B
ASP
114
B
ASP
79
6
1_555
B
ASN
131
B
ASN
96
6
10_556
B
HOH
316
X
HOH
6
1_555
B
HOH
324
X
HOH
6
1_555
A
LYS
48
A
LYS
13
5
1_555
B
ARG
52
B
ARG
17
5
1_555
B
CYS
106
B
CYS
71
5
1_555
B
TYR
108
B
TYR
73
5
1_555
B
HOH
322
X
HOH
5
1_555
B
THR
75
B
THR
40
5
1_555
B
LYS
76
B
LYS
41
5
1_555
B
ASP
139
B
ASP
104
5
1_555
B
ASP
141
B
ASP
106
5
1_555
B
ASN
143
B
ASN
108
5
1_555
B
GLY
45
B
GLY
10
1
1_555
A
GOL
207
I
GOL
2
1_555
B
LYS
48
B
LYS
13
2
1_555
B
GLU
84
B
GLU
49
3
1_555
B
GLU
85
B
GLU
50
3
1_555
B
HOH
314
X
HOH
3
1_555
B
ASN
133
B
ASN
98
1
1_555
B
GLN
111
B
GLN
76
3
1_555
B
GLY
120
B
GLY
85
3
1_555
B
HOH
329
X
HOH
3
1_555
B
LYS
117
B
LYS
82
3
1_555
B
GLU
140
B
GLU
105
3
1_555
B
HOH
317
X
HOH
3
1_555
B
GLN
97
B
GLN
62
1
1_555
A
LYS
53
A
LYS
18
7
8_446
A
GLU
57
A
GLU
22
7
8_446
B
GLN
54
B
GLN
19
7
1_555
B
ARG
73
B
ARG
38
7
1_555
B
ASP
141
B
ASP
106
7
1_555
B
ASN
143
B
ASN
108
7
1_555
B
HOH
330
X
HOH
7
1_555
179
P 65 2 2