0.015113
0.000000
0.006499
0.000000
0.020653
0.000000
0.000000
0.000000
0.024401
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
113.27
90.00
66.170
48.420
44.610
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
Ca 2
40.078
CALCIUM ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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 calcium-regulated periplasmic protein of unknown function (NP_809836.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.40 A resolution
10.2210/pdb3db7/pdb
pdb_00003db7
100
1
Flat mirror (vertical focusing)
CCD
2008-03-04
MARMOSAIC 325 mm CCD
Single crystal Si(111) bent monochromator (horizontal focusing)
MAD
M
x-ray
1
0.91837
1.0
0.97947
1.0
0.97891
1.0
BL11-1
SSRL
0.91837,0.97947,0.97891
SYNCHROTRON
SSRL BEAMLINE BL11-1
14790.481
putative calcium-regulated periplasmic protein
1
man
polymer
40.078
CALCIUM ION
3
syn
non-polymer
62.068
1,2-ETHANEDIOL
2
syn
non-polymer
18.015
water
194
nat
water
no
yes
GADDDKPIQVTQ(MSE)PQLAQQFIKQHFSDSKVALAK(MSE)ESDFLYKSYEVIFTNGNKVEFDKKGNWEEVDCKHTSV
PVAIIPAAIQKYVTTNYPDAKVLKIERDKKDYEVKLSNRTELKFDLKFNLIDIDN
GADDDKPIQVTQMPQLAQQFIKQHFSDSKVALAKMESDFLYKSYEVIFTNGNKVEFDKKGNWEEVDCKHTSVPVAIIPAA
IQKYVTTNYPDAKVLKIERDKKDYEVKLSNRTELKFDLKFNLIDIDN
A
389981
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
sample
NP_809836.1, BT_0923
818
Bacteroides thetaiotaomicron
562
Escherichia coli
HK100
Plasmid
SpeedET
1
2.22
44.58
VAPOR DIFFUSION, SITTING DROP
7.3
0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7., NANODROP, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
pdbx_struct_assembly_auth_evidence
software
pdbx_struct_special_symmetry
software
struct_conn
database_2
pdbx_struct_conn_angle
struct_conn
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
2008-10-28
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
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_alt_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_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
2008-05-30
REL
REL
CA
CALCIUM ION
EDO
1,2-ETHANEDIOL
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. THE CLONED CONSTRUCT CONTAINS RESIDUES 20-145 OF THE FULL LENGTH PROTEIN.
CA
1
2
CA
CA
1
A
CA
2
2
CA
CA
2
A
CA
3
2
CA
CA
3
A
EDO
4
3
EDO
EDO
4
A
EDO
5
3
EDO
EDO
5
A
HOH
6
4
HOH
HOH
146
A
HOH
7
4
HOH
HOH
147
A
HOH
8
4
HOH
HOH
148
A
HOH
9
4
HOH
HOH
149
A
HOH
10
4
HOH
HOH
150
A
HOH
11
4
HOH
HOH
151
A
HOH
12
4
HOH
HOH
152
A
HOH
13
4
HOH
HOH
153
A
HOH
14
4
HOH
HOH
154
A
HOH
15
4
HOH
HOH
155
A
HOH
16
4
HOH
HOH
156
A
HOH
17
4
HOH
HOH
157
A
HOH
18
4
HOH
HOH
158
A
HOH
19
4
HOH
HOH
159
A
HOH
20
4
HOH
HOH
160
A
HOH
21
4
HOH
HOH
161
A
HOH
22
4
HOH
HOH
162
A
HOH
23
4
HOH
HOH
163
A
HOH
24
4
HOH
HOH
164
A
HOH
25
4
HOH
HOH
165
A
HOH
26
4
HOH
HOH
166
A
HOH
27
4
HOH
HOH
167
A
HOH
28
4
HOH
HOH
168
A
HOH
29
4
HOH
HOH
169
A
HOH
30
4
HOH
HOH
170
A
HOH
31
4
HOH
HOH
171
A
HOH
32
4
HOH
HOH
172
A
HOH
33
4
HOH
HOH
173
A
HOH
34
4
HOH
HOH
174
A
HOH
35
4
HOH
HOH
175
A
HOH
36
4
HOH
HOH
176
A
HOH
37
4
HOH
HOH
177
A
HOH
38
4
HOH
HOH
178
A
HOH
39
4
HOH
HOH
179
A
HOH
40
4
HOH
HOH
180
A
HOH
41
4
HOH
HOH
181
A
HOH
42
4
HOH
HOH
182
A
HOH
43
4
HOH
HOH
183
A
HOH
44
4
HOH
HOH
184
A
HOH
45
4
HOH
HOH
185
A
HOH
46
4
HOH
HOH
186
A
HOH
47
4
HOH
HOH
187
A
HOH
48
4
HOH
HOH
188
A
HOH
49
4
HOH
HOH
189
A
HOH
50
4
HOH
HOH
190
A
HOH
51
4
HOH
HOH
191
A
HOH
52
4
HOH
HOH
192
A
HOH
53
4
HOH
HOH
193
A
HOH
54
4
HOH
HOH
194
A
HOH
55
4
HOH
HOH
195
A
HOH
56
4
HOH
HOH
196
A
HOH
57
4
HOH
HOH
197
A
HOH
58
4
HOH
HOH
198
A
HOH
59
4
HOH
HOH
199
A
HOH
60
4
HOH
HOH
200
A
HOH
61
4
HOH
HOH
201
A
HOH
62
4
HOH
HOH
202
A
HOH
63
4
HOH
HOH
203
A
HOH
64
4
HOH
HOH
204
A
HOH
65
4
HOH
HOH
205
A
HOH
66
4
HOH
HOH
206
A
HOH
67
4
HOH
HOH
207
A
HOH
68
4
HOH
HOH
208
A
HOH
69
4
HOH
HOH
209
A
HOH
70
4
HOH
HOH
210
A
HOH
71
4
HOH
HOH
211
A
HOH
72
4
HOH
HOH
212
A
HOH
73
4
HOH
HOH
213
A
HOH
74
4
HOH
HOH
214
A
HOH
75
4
HOH
HOH
215
A
HOH
76
4
HOH
HOH
216
A
HOH
77
4
HOH
HOH
217
A
HOH
78
4
HOH
HOH
218
A
HOH
79
4
HOH
HOH
219
A
HOH
80
4
HOH
HOH
220
A
HOH
81
4
HOH
HOH
221
A
HOH
82
4
HOH
HOH
222
A
HOH
83
4
HOH
HOH
223
A
HOH
84
4
HOH
HOH
224
A
HOH
85
4
HOH
HOH
225
A
HOH
86
4
HOH
HOH
226
A
HOH
87
4
HOH
HOH
227
A
HOH
88
4
HOH
HOH
228
A
HOH
89
4
HOH
HOH
229
A
HOH
90
4
HOH
HOH
230
A
HOH
91
4
HOH
HOH
231
A
HOH
92
4
HOH
HOH
232
A
HOH
93
4
HOH
HOH
233
A
HOH
94
4
HOH
HOH
234
A
HOH
95
4
HOH
HOH
235
A
HOH
96
4
HOH
HOH
236
A
HOH
97
4
HOH
HOH
237
A
HOH
98
4
HOH
HOH
238
A
HOH
99
4
HOH
HOH
239
A
HOH
100
4
HOH
HOH
240
A
HOH
101
4
HOH
HOH
241
A
HOH
102
4
HOH
HOH
242
A
HOH
103
4
HOH
HOH
243
A
HOH
104
4
HOH
HOH
244
A
HOH
105
4
HOH
HOH
245
A
HOH
106
4
HOH
HOH
246
A
HOH
107
4
HOH
HOH
247
A
HOH
108
4
HOH
HOH
248
A
HOH
109
4
HOH
HOH
249
A
HOH
110
4
HOH
HOH
250
A
HOH
111
4
HOH
HOH
251
A
HOH
112
4
HOH
HOH
252
A
HOH
113
4
HOH
HOH
253
A
HOH
114
4
HOH
HOH
254
A
HOH
115
4
HOH
HOH
255
A
HOH
116
4
HOH
HOH
256
A
HOH
117
4
HOH
HOH
257
A
HOH
118
4
HOH
HOH
258
A
HOH
119
4
HOH
HOH
259
A
HOH
120
4
HOH
HOH
260
A
HOH
121
4
HOH
HOH
261
A
HOH
122
4
HOH
HOH
262
A
HOH
123
4
HOH
HOH
263
A
HOH
124
4
HOH
HOH
264
A
HOH
125
4
HOH
HOH
265
A
HOH
126
4
HOH
HOH
266
A
HOH
127
4
HOH
HOH
267
A
HOH
128
4
HOH
HOH
268
A
HOH
129
4
HOH
HOH
269
A
HOH
130
4
HOH
HOH
270
A
HOH
131
4
HOH
HOH
271
A
HOH
132
4
HOH
HOH
272
A
HOH
133
4
HOH
HOH
273
A
HOH
134
4
HOH
HOH
274
A
HOH
135
4
HOH
HOH
275
A
HOH
136
4
HOH
HOH
276
A
HOH
137
4
HOH
HOH
277
A
HOH
138
4
HOH
HOH
278
A
HOH
139
4
HOH
HOH
279
A
HOH
140
4
HOH
HOH
280
A
HOH
141
4
HOH
HOH
281
A
HOH
142
4
HOH
HOH
282
A
HOH
143
4
HOH
HOH
283
A
HOH
144
4
HOH
HOH
284
A
HOH
145
4
HOH
HOH
285
A
HOH
146
4
HOH
HOH
286
A
HOH
147
4
HOH
HOH
287
A
HOH
148
4
HOH
HOH
288
A
HOH
149
4
HOH
HOH
289
A
HOH
150
4
HOH
HOH
290
A
HOH
151
4
HOH
HOH
291
A
HOH
152
4
HOH
HOH
292
A
HOH
153
4
HOH
HOH
293
A
HOH
154
4
HOH
HOH
294
A
HOH
155
4
HOH
HOH
295
A
HOH
156
4
HOH
HOH
296
A
HOH
157
4
HOH
HOH
297
A
HOH
158
4
HOH
HOH
298
A
HOH
159
4
HOH
HOH
299
A
HOH
160
4
HOH
HOH
300
A
HOH
161
4
HOH
HOH
301
A
HOH
162
4
HOH
HOH
302
A
HOH
163
4
HOH
HOH
303
A
HOH
164
4
HOH
HOH
304
A
HOH
165
4
HOH
HOH
305
A
HOH
166
4
HOH
HOH
306
A
HOH
167
4
HOH
HOH
307
A
HOH
168
4
HOH
HOH
308
A
HOH
169
4
HOH
HOH
309
A
HOH
170
4
HOH
HOH
310
A
HOH
171
4
HOH
HOH
311
A
HOH
172
4
HOH
HOH
312
A
HOH
173
4
HOH
HOH
313
A
HOH
174
4
HOH
HOH
314
A
HOH
175
4
HOH
HOH
315
A
HOH
176
4
HOH
HOH
316
A
HOH
177
4
HOH
HOH
317
A
HOH
178
4
HOH
HOH
318
A
HOH
179
4
HOH
HOH
319
A
HOH
180
4
HOH
HOH
320
A
HOH
181
4
HOH
HOH
321
A
HOH
182
4
HOH
HOH
322
A
HOH
183
4
HOH
HOH
323
A
HOH
184
4
HOH
HOH
324
A
HOH
185
4
HOH
HOH
325
A
HOH
186
4
HOH
HOH
326
A
HOH
187
4
HOH
HOH
327
A
HOH
188
4
HOH
HOH
328
A
HOH
189
4
HOH
HOH
329
A
HOH
190
4
HOH
HOH
330
A
HOH
191
4
HOH
HOH
331
A
HOH
192
4
HOH
HOH
332
A
HOH
193
4
HOH
HOH
333
A
HOH
194
4
HOH
HOH
334
A
HOH
195
4
HOH
HOH
335
A
HOH
196
4
HOH
HOH
336
A
HOH
197
4
HOH
HOH
337
A
HOH
198
4
HOH
HOH
338
A
HOH
199
4
HOH
HOH
339
A
GLY
0
n
1
GLY
0
A
ALA
20
n
2
ALA
20
A
ASP
21
n
3
ASP
21
A
ASP
22
n
4
ASP
22
A
ASP
23
n
5
ASP
23
A
LYS
24
n
6
LYS
24
A
PRO
25
n
7
PRO
25
A
ILE
26
n
8
ILE
26
A
GLN
27
n
9
GLN
27
A
VAL
28
n
10
VAL
28
A
THR
29
n
11
THR
29
A
GLN
30
n
12
GLN
30
A
MSE
31
n
13
MSE
31
A
PRO
32
n
14
PRO
32
A
GLN
33
n
15
GLN
33
A
LEU
34
n
16
LEU
34
A
ALA
35
n
17
ALA
35
A
GLN
36
n
18
GLN
36
A
GLN
37
n
19
GLN
37
A
PHE
38
n
20
PHE
38
A
ILE
39
n
21
ILE
39
A
LYS
40
n
22
LYS
40
A
GLN
41
n
23
GLN
41
A
HIS
42
n
24
HIS
42
A
PHE
43
n
25
PHE
43
A
SER
44
n
26
SER
44
A
ASP
45
n
27
ASP
45
A
SER
46
n
28
SER
46
A
LYS
47
n
29
LYS
47
A
VAL
48
n
30
VAL
48
A
ALA
49
n
31
ALA
49
A
LEU
50
n
32
LEU
50
A
ALA
51
n
33
ALA
51
A
LYS
52
n
34
LYS
52
A
MSE
53
n
35
MSE
53
A
GLU
54
n
36
GLU
54
A
SER
55
n
37
SER
55
A
ASP
56
n
38
ASP
56
A
PHE
57
n
39
PHE
57
A
LEU
58
n
40
LEU
58
A
TYR
59
n
41
TYR
59
A
LYS
60
n
42
LYS
60
A
SER
61
n
43
SER
61
A
TYR
62
n
44
TYR
62
A
GLU
63
n
45
GLU
63
A
VAL
64
n
46
VAL
64
A
ILE
65
n
47
ILE
65
A
PHE
66
n
48
PHE
66
A
THR
67
n
49
THR
67
A
ASN
68
n
50
ASN
68
A
GLY
69
n
51
GLY
69
A
ASN
70
n
52
ASN
70
A
LYS
71
n
53
LYS
71
A
VAL
72
n
54
VAL
72
A
GLU
73
n
55
GLU
73
A
PHE
74
n
56
PHE
74
A
ASP
75
n
57
ASP
75
A
LYS
76
n
58
LYS
76
A
LYS
77
n
59
LYS
77
A
GLY
78
n
60
GLY
78
A
ASN
79
n
61
ASN
79
A
TRP
80
n
62
TRP
80
A
GLU
81
n
63
GLU
81
A
GLU
82
n
64
GLU
82
A
VAL
83
n
65
VAL
83
A
ASP
84
n
66
ASP
84
A
CYS
85
n
67
CYS
85
A
LYS
86
n
68
LYS
86
A
HIS
87
n
69
HIS
87
A
THR
88
n
70
THR
88
A
SER
89
n
71
SER
89
A
VAL
90
n
72
VAL
90
A
PRO
91
n
73
PRO
91
A
VAL
92
n
74
VAL
92
A
ALA
93
n
75
ALA
93
A
ILE
94
n
76
ILE
94
A
ILE
95
n
77
ILE
95
A
PRO
96
n
78
PRO
96
A
ALA
97
n
79
ALA
97
A
ALA
98
n
80
ALA
98
A
ILE
99
n
81
ILE
99
A
GLN
100
n
82
GLN
100
A
LYS
101
n
83
LYS
101
A
TYR
102
n
84
TYR
102
A
VAL
103
n
85
VAL
103
A
THR
104
n
86
THR
104
A
THR
105
n
87
THR
105
A
ASN
106
n
88
ASN
106
A
TYR
107
n
89
TYR
107
A
PRO
108
n
90
PRO
108
A
ASP
109
n
91
ASP
109
A
ALA
110
n
92
ALA
110
A
LYS
111
n
93
LYS
111
A
VAL
112
n
94
VAL
112
A
LEU
113
n
95
LEU
113
A
LYS
114
n
96
LYS
114
A
ILE
115
n
97
ILE
115
A
GLU
116
n
98
GLU
116
A
ARG
117
n
99
ARG
117
A
ASP
118
n
100
ASP
118
A
LYS
119
n
101
LYS
119
A
LYS
120
n
102
LYS
120
A
ASP
121
n
103
ASP
121
A
TYR
122
n
104
TYR
122
A
GLU
123
n
105
GLU
123
A
VAL
124
n
106
VAL
124
A
LYS
125
n
107
LYS
125
A
LEU
126
n
108
LEU
126
A
SER
127
n
109
SER
127
A
ASN
128
n
110
ASN
128
A
ARG
129
n
111
ARG
129
A
THR
130
n
112
THR
130
A
GLU
131
n
113
GLU
131
A
LEU
132
n
114
LEU
132
A
LYS
133
n
115
LYS
133
A
PHE
134
n
116
PHE
134
A
ASP
135
n
117
ASP
135
A
LEU
136
n
118
LEU
136
A
LYS
137
n
119
LYS
137
A
PHE
138
n
120
PHE
138
A
ASN
139
n
121
ASN
139
A
LEU
140
n
122
LEU
140
A
ILE
141
n
123
ILE
141
A
ASP
142
n
124
ASP
142
A
ILE
143
n
125
ILE
143
A
ASP
144
n
126
ASP
144
A
ASN
145
n
127
ASN
145
A
1.2557
0.0120
0.1457
0.3124
0.0582
0.4953
0.0117
-0.0362
-0.0013
0.0069
-0.0177
-0.0076
0.0011
0.0328
0.0060
-0.0143
-0.0043
-0.0026
-0.0308
0.0052
-0.0250
refined
5.4168
48.0223
9.8704
X-RAY DIFFRACTION
A
0
A
1
A
145
A
127
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
2
dimeric
author_defined_assembly
1
monomeric
gel filtration
light scattering
gel filtration
light scattering
3320
-77
12730
A
GLU
54
A
OE1
GLU
36
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
54
A
OE2
GLU
36
1_555
50.3
A
GLU
54
A
OE1
GLU
36
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
63
A
OE2
GLU
45
1_555
76.4
A
GLU
54
A
OE2
GLU
36
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
63
A
OE2
GLU
45
1_555
126.6
A
GLU
54
A
OE1
GLU
36
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE1
GLU
55
1_555
127.7
A
GLU
54
A
OE2
GLU
36
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE1
GLU
55
1_555
129.1
A
GLU
63
A
OE2
GLU
45
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE1
GLU
55
1_555
79.3
A
GLU
54
A
OE1
GLU
36
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE2
GLU
55
1_555
81.6
A
GLU
54
A
OE2
GLU
36
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE2
GLU
55
1_555
81.7
A
GLU
63
A
OE2
GLU
45
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE2
GLU
55
1_555
89.8
A
GLU
73
A
OE1
GLU
55
1_555
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE2
GLU
55
1_555
52.6
A
GLU
73
A
OE1
GLU
55
1_555
A
CA
2
C
CA
CA
1_555
A
GLU
82
A
OE1
GLU
64
1_555
90.5
A
GLU
73
A
OE1
GLU
55
1_555
A
CA
2
C
CA
CA
1_555
A
HOH
146
G
O
HOH
1_555
80.1
A
GLU
82
A
OE1
GLU
64
1_555
A
CA
2
C
CA
CA
1_555
A
HOH
146
G
O
HOH
1_555
105.2
A
GLU
73
A
OE1
GLU
55
1_555
A
CA
2
C
CA
CA
1_555
A
HOH
158
G
O
HOH
1_555
153.2
A
GLU
82
A
OE1
GLU
64
1_555
A
CA
2
C
CA
CA
1_555
A
HOH
158
G
O
HOH
1_555
85.6
A
HOH
146
G
O
HOH
1_555
A
CA
2
C
CA
CA
1_555
A
HOH
158
G
O
HOH
1_555
75.4
A
EDO
5
A
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
EDO
5
B
F
O2
EDO
1_555
19.1
A
EDO
5
A
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
EDO
5
A
F
O1
EDO
1_555
60.8
A
EDO
5
B
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
EDO
5
A
F
O1
EDO
1_555
73.5
A
EDO
5
A
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
GLU
123
A
A
OE2
GLU
105
1_555
68.0
A
EDO
5
B
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
GLU
123
A
A
OE2
GLU
105
1_555
80.2
A
EDO
5
A
F
O1
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
GLU
123
A
A
OE2
GLU
105
1_555
91.2
A
EDO
5
A
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
336
B
G
O
HOH
1_555
100.4
A
EDO
5
B
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
336
B
G
O
HOH
1_555
104.8
A
EDO
5
A
F
O1
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
336
B
G
O
HOH
1_555
45.3
A
GLU
123
A
A
OE2
GLU
105
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
336
B
G
O
HOH
1_555
128.5
A
EDO
5
A
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
A
G
O
HOH
1_555
131.1
A
EDO
5
B
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
A
G
O
HOH
1_555
146.9
A
EDO
5
A
F
O1
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
A
G
O
HOH
1_555
73.5
A
GLU
123
A
A
OE2
GLU
105
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
A
G
O
HOH
1_555
98.0
A
HOH
336
B
G
O
HOH
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
A
G
O
HOH
1_555
50.9
A
EDO
5
A
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
B
G
O
HOH
1_555
95.4
A
EDO
5
B
F
O2
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
B
G
O
HOH
1_555
114.3
A
EDO
5
A
F
O1
EDO
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
B
G
O
HOH
1_555
67.8
A
GLU
123
A
A
OE2
GLU
105
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
B
G
O
HOH
1_555
50.8
A
HOH
336
B
G
O
HOH
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
B
G
O
HOH
1_555
82.9
A
HOH
337
A
G
O
HOH
1_555
A
CA
3
D
CA
CA
1_555
A
HOH
337
B
G
O
HOH
1_555
48.9
A
MSE
31
SELENOMETHIONINE
A
MSE
13
MET
A
MSE
53
SELENOMETHIONINE
A
MSE
35
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
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
LYS
24
A
N
LYS
6
A
O
MSE
53
A
O
MSE
35
A
N
LEU
50
A
N
LEU
32
A
O
ILE
65
A
O
ILE
47
A
N
TYR
62
A
N
TYR
44
A
O
PHE
74
A
O
PHE
56
A
N
LYS
71
A
N
LYS
53
A
O
ASP
84
A
O
ASP
66
A
N
VAL
83
A
N
VAL
65
A
O
ILE
115
A
O
ILE
97
A
N
LEU
113
A
N
LEU
95
A
O
LYS
125
A
O
LYS
107
A
N
TYR
122
A
N
TYR
104
A
O
PHE
134
A
O
PHE
116
A
N
LYS
133
A
N
LYS
115
A
O
ILE
141
A
O
ILE
123
1
A
CA
3
D
CA
1
A
HOH
334
G
HOH
1
A
CD
LYS
24
A
CD
LYS
6
1
Y
1
A
CE
LYS
24
A
CE
LYS
6
1
Y
1
A
NZ
LYS
24
A
NZ
LYS
6
1
Y
1
A
CG
ASP
45
A
CG
ASP
27
1
Y
1
A
OD1
ASP
45
A
OD1
ASP
27
1
Y
1
A
OD2
ASP
45
A
OD2
ASP
27
1
Y
1
A
CD
LYS
47
A
CD
LYS
29
1
Y
1
A
CE
LYS
47
A
CE
LYS
29
1
Y
1
A
NZ
LYS
47
A
NZ
LYS
29
1
Y
1
A
CD
LYS
60
A
CD
LYS
42
1
Y
1
A
CE
LYS
60
A
CE
LYS
42
1
Y
1
A
NZ
LYS
60
A
NZ
LYS
42
1
Y
1
A
NZ
LYS
76
A
NZ
LYS
58
1
Y
1
A
CE
LYS
77
A
CE
LYS
59
1
Y
1
A
NZ
LYS
77
A
NZ
LYS
59
1
Y
1
A
CE
LYS
111
A
CE
LYS
93
1
Y
1
A
NZ
LYS
111
A
NZ
LYS
93
1
Y
1
A
CE
LYS
120
A
CE
LYS
102
1
Y
1
A
NZ
LYS
120
A
NZ
LYS
102
1
Y
1
A
CZ
ARG
129
A
CZ
ARG
111
1
Y
1
A
NH1
ARG
129
A
NH1
ARG
111
1
Y
1
A
NH2
ARG
129
A
NH2
ARG
111
1
Y
1
A
THR
88
-136.51
-108.94
1
A
ARG
129
84.18
-6.44
10.575
-0.28
0.00
0.15
0.24
0.00
0.17
0.969
0.955
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.ETHYLENE GLYCOL AND CALCIUM IONS FROM THE CRYSTALLIZATION COND ARE MODELED IN THIS STRUCTURE.
0.19824
0.16034
0.16228
1.40
24.922
1172
23150
5.1
90.53
2.134
0.045
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MAD
0.066
0.071
0.80
0.80
1.20
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.40
24.922
194
1218
11
0
1013
0.018
0.022
1131
0.001
0.020
771
1.559
1.965
1539
1.096
3.000
1902
6.603
5.000
146
35.122
26.731
52
11.482
15.000
209
11.545
15.000
1
0.102
0.200
168
0.008
0.021
1293
0.003
0.020
207
1.626
3.000
697
0.510
3.000
271
2.615
5.000
1150
3.931
8.000
434
5.984
11.000
389
0.299
0.258
1.437
76
1644
20
91.98
1.40
24.922
3DB7
23150
-3.00
0.042
1
10.440
2.149
90.5
0.536
1.40
1.45
1.5
1
0.369
1.45
1.51
2.0
1
0.281
1.51
1.58
2.7
1
0.211
1.58
1.66
3.6
1
0.155
1.66
1.76
4.8
1
0.093
1.76
1.90
7.4
1
0.046
1.90
2.09
12.4
1
0.036
2.09
2.39
16.0
1
0.027
2.39
3.01
20.8
1
0.017
3.01
24.92
32.1
1
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.4.0067
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
George 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/xscale_program.html
XSCALE
package
data extraction
PDB
sw-help@rcsb.rutgers.edu
September 10, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.004
data reduction
XDS
phasing
SHELXD
phasing
autoSHARP
Crystal structure of a putative calcium-regulated periplasmic protein (bt0923) from bacteroides thetaiotaomicron at 1.40 A resolution
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
AUTHORS STATE THAT ONLY WHEN CA1 AND CA2 ARE INCLUDED IN THE CALCULATION, DOES PISA (v1.14) PREDICT THAT A STABLE DIMER COULD BE A
PROBABLE QUATERNARY STRUCTURE. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING (SEC+SLS) WITHOUT ADDED CALCIUM SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. WHEN A SAMPLE WAS RUN WITH 0.2 M CALCIUM CHLORIDE IN THE MOBILE PHASE (SIMILAR CONCENTRATION TO THAT IN THE CRYSTALLIZATION REAGENT), THE SEC+SLS RESULTS SHOWED PRIMARILY DIMER.
A
GLY
0
A
GLY
1
HELX_P
A
ASP
23
A
ASP
5
5
1
5
A
GLN
27
A
GLN
9
HELX_P
A
MSE
31
A
MSE
13
5
2
5
A
PRO
32
A
PRO
14
HELX_P
A
PHE
43
A
PHE
25
1
3
12
A
PRO
91
A
PRO
73
HELX_P
A
ILE
95
A
ILE
77
5
4
5
A
PRO
96
A
PRO
78
HELX_P
A
TYR
107
A
TYR
89
1
5
12
covale
1.331
both
A
A
GLN
30
A
C
GLN
12
1_555
A
MSE
31
A
N
MSE
13
1_555
covale
1.313
both
B
A
GLN
30
A
C
GLN
12
1_555
A
MSE
31
A
N
MSE
13
1_555
covale
1.348
both
A
A
MSE
31
A
C
MSE
13
1_555
A
PRO
32
A
N
PRO
14
1_555
covale
1.336
both
B
A
MSE
31
A
C
MSE
13
1_555
A
PRO
32
A
N
PRO
14
1_555
covale
1.322
both
A
LYS
52
A
C
LYS
34
1_555
A
MSE
53
A
N
MSE
35
1_555
covale
1.332
both
A
MSE
53
A
C
MSE
35
1_555
A
GLU
54
A
N
GLU
36
1_555
metalc
2.463
A
CA
1
B
CA
CA
1_555
A
GLU
54
A
OE1
GLU
36
1_555
metalc
2.691
A
CA
1
B
CA
CA
1_555
A
GLU
54
A
OE2
GLU
36
1_555
metalc
2.344
A
CA
1
B
CA
CA
1_555
A
GLU
63
A
OE2
GLU
45
1_555
metalc
2.508
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE1
GLU
55
1_555
metalc
2.506
A
CA
1
B
CA
CA
1_555
A
GLU
73
A
OE2
GLU
55
1_555
metalc
2.314
A
CA
2
C
CA
CA
1_555
A
GLU
73
A
OE1
GLU
55
1_555
metalc
2.279
A
CA
2
C
CA
CA
1_555
A
GLU
82
A
OE1
GLU
64
1_555
metalc
2.416
A
CA
2
C
CA
CA
1_555
A
HOH
146
G
O
HOH
1_555
metalc
2.466
A
CA
2
C
CA
CA
1_555
A
HOH
158
G
O
HOH
1_555
metalc
2.497
A
A
CA
3
D
CA
CA
1_555
A
EDO
5
F
O2
EDO
1_555
metalc
2.519
B
A
CA
3
D
CA
CA
1_555
A
EDO
5
F
O2
EDO
1_555
metalc
2.460
A
A
CA
3
D
CA
CA
1_555
A
EDO
5
F
O1
EDO
1_555
metalc
2.292
A
A
CA
3
D
CA
CA
1_555
A
GLU
123
A
OE2
GLU
105
1_555
metalc
2.181
B
A
CA
3
D
CA
CA
1_555
A
HOH
336
G
O
HOH
1_555
metalc
2.386
A
A
CA
3
D
CA
CA
1_555
A
HOH
337
G
O
HOH
1_555
metalc
2.199
B
A
CA
3
D
CA
CA
1_555
A
HOH
337
G
O
HOH
1_555
Ca-BINDING PROTEIN
Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, ca-binding protein
Q8A994_BACTN
UNP
1
20
Q8A994
ADDDKPIQVTQMPQLAQQFIKQHFSDSKVALAKMESDFLYKSYEVIFTNGNKVEFDKKGNWEEVDCKHTSVPVAIIPAAI
QKYVTTNYPDAKVLKIERDKKDYEVKLSNRTELKFDLKFNLIDIDN
20
145
3DB7
20
145
Q8A994
A
1
2
127
1
expression tag
GLY
0
3DB7
A
Q8A994
UNP
1
9
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
24
A
LYS
6
A
ILE
26
A
ILE
8
A
VAL
48
A
VAL
30
A
ASP
56
A
ASP
38
A
TYR
59
A
TYR
41
A
PHE
66
A
PHE
48
A
LYS
71
A
LYS
53
A
PHE
74
A
PHE
56
A
TRP
80
A
TRP
62
A
ASP
84
A
ASP
66
A
VAL
112
A
VAL
94
A
ARG
117
A
ARG
99
A
ASP
121
A
ASP
103
A
LEU
126
A
LEU
108
A
GLU
131
A
GLU
113
A
ASP
135
A
ASP
117
A
LEU
140
A
LEU
122
A
ASP
144
A
ASP
126
BINDING SITE FOR RESIDUE CA A 1
A
CA
1
Software
6
BINDING SITE FOR RESIDUE CA A 2
A
CA
2
Software
6
BINDING SITE FOR RESIDUE CA A 3
A
CA
3
Software
3
BINDING SITE FOR RESIDUE EDO A 4
A
EDO
4
Software
4
BINDING SITE FOR RESIDUE EDO A 5
A
EDO
5
Software
8
A
GLU
54
A
GLU
36
6
1_555
A
GLU
63
A
GLU
45
6
1_555
A
GLU
73
A
GLU
55
6
1_555
A
ASP
142
A
ASP
124
6
2_555
A
ILE
143
A
ILE
125
6
2_555
A
ASP
144
A
ASP
126
6
2_555
A
GLU
73
A
GLU
55
6
1_555
A
GLU
82
A
GLU
64
6
1_555
A
ASP
142
A
ASP
124
6
2_555
A
ASP
144
A
ASP
126
6
2_555
A
HOH
146
G
HOH
6
1_555
A
HOH
158
G
HOH
6
1_555
A
GLU
123
A
GLU
105
3
2_555
A
HOH
336
G
HOH
3
2_555
A
HOH
337
G
HOH
3
2_555
A
ILE
26
A
ILE
8
4
1_555
A
GLN
27
A
GLN
9
4
1_555
A
ALA
51
A
ALA
33
4
1_555
A
LYS
137
A
LYS
119
4
3_545
A
GLU
116
A
GLU
98
8
1_555
A
ARG
117
A
ARG
99
8
1_555
A
ASP
121
A
ASP
103
8
1_555
A
GLU
123
A
GLU
105
8
2_555
A
LYS
133
A
LYS
115
8
2_555
A
HOH
255
G
HOH
8
1_555
A
HOH
336
G
HOH
8
1_555
A
HOH
337
G
HOH
8
2_555
5
C 1 2 1