0.009680
0.005588
0.000000
0.000000
0.011177
0.000000
0.000000
0.000000
0.011010
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
103.311
103.311
90.830
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
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 a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution
10.2210/pdb4qoa/pdb
pdb_00004qoa
100
1
Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
PIXEL
2014-03-27
DECTRIS PILATUS 6M
double crystal Si(111)
MAD
M
x-ray
1
0.9116
1.0
0.9794
1.0
0.9793
1.0
BL12-2
SSRL
0.9116,0.9794,0.9793
SYNCHROTRON
SSRL BEAMLINE BL12-2
14669.667
Putative periplasmic protein
UNP residues 21-146
1
man
polymer
62.068
1,2-ETHANEDIOL
2
syn
non-polymer
18.015
water
17
nat
water
no
yes
GGDVITQDTKQLPLTARNFINQYFSKPHISHIKIESEILQTKKYEVLLTDRTEIDFDKKGNWLEVDCKKSAVPEALIPVP
VKEYVKANFPREIITKIERGRTGVEIELGNDYSLKFNKKGKFVS(MSE)DD
GGDVITQDTKQLPLTARNFINQYFSKPHISHIKIESEILQTKKYEVLLTDRTEIDFDKKGNWLEVDCKKSAVPEALIPVP
VKEYVKANFPREIITKIERGRTGVEIELGNDYSLKFNKKGKFVSMDD
A
JCSG-417915
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
8492
BACUNI_04550
411479
Bacteroides uniformis
562
Escherichia coli
PB1
Plasmid
SpeedET
1
4.77
74.21
VAPOR DIFFUSION, SITTING DROP
24.00% polyethylene glycol 3350, 0.16M tri-ammonium citrate, 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
Refinement description
Database references
Derived calculations
1
0
2014-07-16
1
1
2017-11-22
1
2
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
2014-06-19
REL
REL
EDO
1,2-ETHANEDIOL
HOH
water
THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING GLY 0 FOLLOWED BY RESIDUES 21-146 OF THE TARGET SEQUENCE.
EDO
147
2
EDO
EDO
201
A
EDO
148
2
EDO
EDO
202
A
HOH
149
3
HOH
HOH
301
A
HOH
150
3
HOH
HOH
302
A
HOH
151
3
HOH
HOH
303
A
HOH
152
3
HOH
HOH
304
A
HOH
153
3
HOH
HOH
305
A
HOH
154
3
HOH
HOH
306
A
HOH
155
3
HOH
HOH
307
A
HOH
156
3
HOH
HOH
308
A
HOH
157
3
HOH
HOH
309
A
HOH
158
3
HOH
HOH
310
A
HOH
159
3
HOH
HOH
311
A
HOH
160
3
HOH
HOH
312
A
HOH
161
3
HOH
HOH
313
A
HOH
162
3
HOH
HOH
314
A
HOH
163
3
HOH
HOH
315
A
HOH
164
3
HOH
HOH
316
A
HOH
165
3
HOH
HOH
317
A
n
1
0
A
GLY
21
n
2
GLY
21
A
ASP
22
n
3
ASP
22
A
VAL
23
n
4
VAL
23
A
ILE
24
n
5
ILE
24
A
THR
25
n
6
THR
25
A
GLN
26
n
7
GLN
26
A
ASP
27
n
8
ASP
27
A
THR
28
n
9
THR
28
A
LYS
29
n
10
LYS
29
A
GLN
30
n
11
GLN
30
A
LEU
31
n
12
LEU
31
A
PRO
32
n
13
PRO
32
A
LEU
33
n
14
LEU
33
A
THR
34
n
15
THR
34
A
ALA
35
n
16
ALA
35
A
ARG
36
n
17
ARG
36
A
ASN
37
n
18
ASN
37
A
PHE
38
n
19
PHE
38
A
ILE
39
n
20
ILE
39
A
ASN
40
n
21
ASN
40
A
GLN
41
n
22
GLN
41
A
TYR
42
n
23
TYR
42
A
PHE
43
n
24
PHE
43
A
SER
44
n
25
SER
44
A
LYS
45
n
26
LYS
45
A
PRO
46
n
27
PRO
46
A
HIS
47
n
28
HIS
47
A
ILE
48
n
29
ILE
48
A
SER
49
n
30
SER
49
A
HIS
50
n
31
HIS
50
A
ILE
51
n
32
ILE
51
A
LYS
52
n
33
LYS
52
A
ILE
53
n
34
ILE
53
A
GLU
54
n
35
GLU
54
A
SER
55
n
36
SER
55
A
GLU
56
n
37
GLU
56
A
ILE
57
n
38
ILE
57
A
LEU
58
n
39
LEU
58
A
GLN
59
n
40
GLN
59
A
THR
60
n
41
THR
60
A
LYS
61
n
42
LYS
61
A
LYS
62
n
43
LYS
62
A
TYR
63
n
44
TYR
63
A
GLU
64
n
45
GLU
64
A
VAL
65
n
46
VAL
65
A
LEU
66
n
47
LEU
66
A
LEU
67
n
48
LEU
67
A
THR
68
n
49
THR
68
A
ASP
69
n
50
ASP
69
A
ARG
70
n
51
ARG
70
A
THR
71
n
52
THR
71
A
GLU
72
n
53
GLU
72
A
ILE
73
n
54
ILE
73
A
ASP
74
n
55
ASP
74
A
PHE
75
n
56
PHE
75
A
ASP
76
n
57
ASP
76
A
LYS
77
n
58
LYS
77
A
LYS
78
n
59
LYS
78
A
GLY
79
n
60
GLY
79
A
ASN
80
n
61
ASN
80
A
TRP
81
n
62
TRP
81
A
LEU
82
n
63
LEU
82
A
GLU
83
n
64
GLU
83
A
VAL
84
n
65
VAL
84
A
ASP
85
n
66
ASP
85
A
CYS
86
n
67
CYS
86
A
LYS
87
n
68
LYS
87
A
LYS
88
n
69
LYS
88
A
SER
89
n
70
SER
89
A
ALA
90
n
71
ALA
90
A
VAL
91
n
72
VAL
91
A
PRO
92
n
73
PRO
92
A
GLU
93
n
74
GLU
93
A
ALA
94
n
75
ALA
94
A
LEU
95
n
76
LEU
95
A
ILE
96
n
77
ILE
96
A
PRO
97
n
78
PRO
97
A
VAL
98
n
79
VAL
98
A
PRO
99
n
80
PRO
99
A
VAL
100
n
81
VAL
100
A
LYS
101
n
82
LYS
101
A
GLU
102
n
83
GLU
102
A
TYR
103
n
84
TYR
103
A
VAL
104
n
85
VAL
104
A
LYS
105
n
86
LYS
105
A
ALA
106
n
87
ALA
106
A
ASN
107
n
88
ASN
107
A
PHE
108
n
89
PHE
108
A
PRO
109
n
90
PRO
109
A
ARG
110
n
91
ARG
110
A
GLU
111
n
92
GLU
111
A
ILE
112
n
93
ILE
112
A
ILE
113
n
94
ILE
113
A
THR
114
n
95
THR
114
A
LYS
115
n
96
LYS
115
A
ILE
116
n
97
ILE
116
A
GLU
117
n
98
GLU
117
A
ARG
118
n
99
ARG
118
A
GLY
119
n
100
GLY
119
A
ARG
120
n
101
ARG
120
A
THR
121
n
102
THR
121
A
GLY
122
n
103
GLY
122
A
VAL
123
n
104
VAL
123
A
GLU
124
n
105
GLU
124
A
ILE
125
n
106
ILE
125
A
GLU
126
n
107
GLU
126
A
LEU
127
n
108
LEU
127
A
GLY
128
n
109
GLY
128
A
ASN
129
n
110
ASN
129
A
ASP
130
n
111
ASP
130
A
TYR
131
n
112
TYR
131
A
SER
132
n
113
SER
132
A
LEU
133
n
114
LEU
133
A
LYS
134
n
115
LYS
134
A
PHE
135
n
116
PHE
135
A
ASN
136
n
117
ASN
136
A
LYS
137
n
118
LYS
137
A
LYS
138
n
119
LYS
138
A
GLY
139
n
120
GLY
139
A
LYS
140
n
121
LYS
140
A
PHE
141
n
122
PHE
141
A
VAL
142
n
123
VAL
142
A
SER
143
n
124
SER
143
A
MSE
144
n
125
MSE
144
A
ASP
145
n
126
ASP
145
A
ASP
146
n
127
ASP
146
A
1.8469
-1.3048
-1.6263
2.0029
1.5563
2.2761
-0.1975
-0.0240
0.1807
0.2042
-0.0189
-0.3548
0.4577
-0.2557
0.2164
-0.1368
0.0861
0.0272
-0.1862
0.0637
0.0583
refined
28.7089
24.7284
28.5723
X-RAY DIFFRACTION
A
21
A
146
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
2
dimeric
4410
-24
15110
A
MSE
144
SELENOMETHIONINE
A
MSE
125
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
7_555
y,x,-z+2/3
crystal symmetry operation
0.0000000000
0.0000000000
60.5533333333
A
N
THR
25
A
N
THR
6
A
O
ILE
51
A
O
ILE
32
A
N
VAL
65
A
N
VAL
46
A
O
ILE
73
A
O
ILE
54
A
N
GLU
72
A
N
GLU
53
A
O
ASP
85
A
O
ASP
66
A
N
VAL
84
A
N
VAL
65
A
O
ILE
116
A
O
ILE
97
A
N
LYS
115
A
N
LYS
96
A
O
GLU
126
A
O
GLU
107
A
N
VAL
123
A
N
VAL
104
A
O
PHE
135
A
O
PHE
116
A
N
LYS
134
A
N
LYS
115
A
O
SER
143
A
O
SER
124
1
A
CG
LYS
45
A
CG
LYS
26
1
Y
1
A
CD
LYS
45
A
CD
LYS
26
1
Y
1
A
CE
LYS
45
A
CE
LYS
26
1
Y
1
A
NZ
LYS
45
A
NZ
LYS
26
1
Y
1
A
CG
ARG
70
A
CG
ARG
51
1
Y
1
A
CD
ARG
70
A
CD
ARG
51
1
Y
1
A
NE
ARG
70
A
NE
ARG
51
1
Y
1
A
CZ
ARG
70
A
CZ
ARG
51
1
Y
1
A
NH1
ARG
70
A
NH1
ARG
51
1
Y
1
A
NH2
ARG
70
A
NH2
ARG
51
1
Y
1
A
CG
LYS
105
A
CG
LYS
86
1
Y
1
A
CD
LYS
105
A
CD
LYS
86
1
Y
1
A
CE
LYS
105
A
CE
LYS
86
1
Y
1
A
NZ
LYS
105
A
NZ
LYS
86
1
Y
1
A
CG
LYS
138
A
CG
LYS
119
1
Y
1
A
CD
LYS
138
A
CD
LYS
119
1
Y
1
A
CE
LYS
138
A
CE
LYS
119
1
Y
1
A
NZ
LYS
138
A
NZ
LYS
119
1
Y
1
A
CG
ASP
146
A
CG
ASP
127
1
Y
1
A
OD1
ASP
146
A
OD1
ASP
127
1
Y
1
A
OD2
ASP
146
A
OD2
ASP
127
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
PRO
46
-96.78
52.31
1
A
SER
49
-100.95
76.96
1
A
HIS
50
74.84
153.68
1
A
LYS
87
58.05
-95.40
1
A
ALA
106
-90.19
-62.79
1
A
VAL
142
-126.39
-62.86
158.890
87.8228
50.710
14.8621
0.0000
0.0000
14.8621
0.0000
-29.7241
0.9249
0.9142
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 THE REFINEMENT. 4. 1,2-ETHANEDIOL USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE.
0.2498
0.2150
0.2166
2.7500
29.823
361
7840
4.6000
99.8300
1.000
0.750
RANDOM
1
THROUGHOUT
0.000
MAD
0.535
2.7500
29.823
17
1030
8
0
1005
487
SINUSOIDAL
6.000
30
HARMONIC
2.000
142
HARMONIC
5.000
1030
HARMONIC
20.000
140
SEMIHARMONIC
5.000
1105
SEMIHARMONIC
4.000
0.009
1030
HARMONIC
2.000
1.170
1389
HARMONIC
2.000
2.490
2.270
0.2982
0.2617
0.2635
3.0700
101
2061
2162
5
4.6700
99.8300
2.75
29.823
4QOA
7860
7860
0.084
1
15.700
9.100
99.800
0.012
2.750
2.820
0.7
5000
565
1.185
1
8.800
100.000
0.012
2.820
2.900
0.7
4393
543
1.054
1
8.100
100.000
0.012
2.900
2.980
1.2
5325
537
0.667
1
9.900
99.900
0.012
2.980
3.070
1.4
5185
520
0.541
1
10.000
100.000
0.012
3.070
3.180
1.7
4835
503
0.453
1
9.600
100.000
0.012
3.180
3.290
2.9
4615
497
0.261
1
9.300
100.000
0.012
3.290
3.410
3.5
4208
466
0.213
1
9.000
99.900
0.012
3.410
3.550
4.7
3691
467
0.156
1
7.900
99.700
0.012
3.550
3.710
6.4
4175
441
0.116
1
9.500
100.000
0.012
3.710
3.890
7.3
4105
423
0.100
1
9.700
100.000
0.012
3.890
4.100
8.8
3904
411
0.078
1
9.500
99.800
0.012
4.100
4.350
10.0
3492
382
0.061
1
9.100
100.000
0.012
4.350
4.650
11.6
3005
364
0.051
1
8.300
100.000
0.012
4.650
5.020
12.7
3135
340
0.050
1
9.200
100.000
0.012
5.020
5.500
11.3
3058
322
0.056
1
9.500
100.000
0.012
5.500
6.150
10.0
2688
291
0.064
1
9.200
99.700
0.012
6.150
7.100
11.4
1962
263
0.056
1
7.500
99.900
0.012
7.100
8.700
14.9
2094
231
0.040
1
9.100
100.000
0.012
8.700
12.300
16.6
1487
179
0.034
1
8.300
99.400
0.012
12.300
29.823
17.7
796
115
0.033
1
6.900
93.100
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
Crystal structure of a putative periplasmic protein (BACUNI_04550) from Bacteroides uniformis ATCC 8492 at 2.75 A resolution
1
N
N
2
N
N
2
N
N
3
N
N
A
ASP
27
A
ASP
8
HELX_P
A
LEU
31
A
LEU
12
5
1
5
A
PRO
32
A
PRO
13
HELX_P
A
PHE
43
A
PHE
24
1
2
12
A
PRO
92
A
PRO
73
HELX_P
A
ILE
96
A
ILE
77
5
3
5
A
PRO
97
A
PRO
78
HELX_P
A
PHE
108
A
PHE
89
1
4
12
covale
1.343
both
A
SER
143
A
C
SER
124
1_555
A
MSE
144
A
N
MSE
125
1_555
covale
1.352
both
A
MSE
144
A
C
MSE
125
1_555
A
ASP
145
A
N
ASP
126
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Two copies of DUF2874 domain (PF11396), BLIP-like fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION
A7VAB9_BACUN
UNP
1
21
A7VAB9
GDVITQDTKQLPLTARNFINQYFSKPHISHIKIESEILQTKKYEVLLTDRTEIDFDKKGNWLEVDCKKSAVPEALIPVPV
KEYVKANFPREIITKIERGRTGVEIELGNDYSLKFNKKGKFVSMDD
21
146
4QOA
21
146
A7VAB9
A
1
2
127
1
expression tag
GLY
0
4QOA
A
A7VAB9
UNP
1
2
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
23
A
VAL
4
A
THR
25
A
THR
6
A
ILE
51
A
ILE
32
A
ILE
53
A
ILE
34
A
LYS
61
A
LYS
42
A
LEU
66
A
LEU
47
A
GLU
72
A
GLU
53
A
ASP
76
A
ASP
57
A
TRP
81
A
TRP
62
A
ASP
85
A
ASP
66
A
ILE
113
A
ILE
94
A
ARG
118
A
ARG
99
A
GLY
122
A
GLY
103
A
LEU
127
A
LEU
108
A
SER
132
A
SER
113
A
ASN
136
A
ASN
117
A
PHE
141
A
PHE
122
A
ASP
145
A
ASP
126
BINDING SITE FOR RESIDUE EDO A 201
A
EDO
201
Software
5
BINDING SITE FOR RESIDUE EDO A 202
A
EDO
202
Software
4
A
PRO
32
A
PRO
13
5
1_555
A
LEU
33
A
LEU
14
5
1_555
A
THR
34
A
THR
15
5
1_555
A
ARG
36
A
ARG
17
5
10_666
A
EDO
202
C
EDO
5
10_666
A
THR
28
A
THR
9
4
1_555
A
ARG
36
A
ARG
17
4
1_555
A
EDO
201
B
EDO
4
10_666
A
HOH
309
D
HOH
4
1_555
179
P 65 2 2