0.017713
0.010226
0.000000
0.000000
0.020453
0.000000
0.000000
0.000000
0.009110
0.00000
0.00000
0.00000
Nosrati, M.
Geiger, J.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
56.457
56.457
109.775
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
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 S
149.211
y
METHIONINE
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
C20 H28 O
284.436
RETINAL
non-polymer
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
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
135
16111
16119
10.1021/ja404900k
24059243
Rational Design of a Colorimetric pH Sensor from a Soluble Retinoic Acid Chaperone.
2013
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
MARMOSAIC 300 mm CCD
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
1.0782
1.0
21-ID-D
APS
1.0782
SYNCHROTRON
APS BEAMLINE 21-ID-D
15650.901
Cellular retinoic acid-binding protein 2
R111K:R132Q:Y134F:T54V:R59W:A32W
1
man
polymer
284.436
RETINAL
1
syn
non-polymer
18.015
water
9
nat
water
Cellular retinoic acid-binding protein II, CRABP-II
no
no
PNFSGNWKIIRSENFEELLKVLGVNVMLRKIWVAAASKPAVEIKQEGDTFYIKVSTTVWTTEINFKVGEEFEEQTVDGRP
CKSLVKWESENKMVCEQKLLKGEGPKTSWTKELTNDGELILTMTADDVVCTQVFVRE
PNFSGNWKIIRSENFEELLKVLGVNVMLRKIWVAAASKPAVEIKQEGDTFYIKVSTTVWTTEINFKVGEEFEEQTVDGRP
CKSLVKWESENKMVCEQKLLKGEGPKTSWTKELTNDGELILTMTADDVVCTQVFVRE
A
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
human
sample
CRABP2
9606
Homo sapiens
562
Escherichia coli
plasmid
pET17b
1
3.23
61.88
VAPOR DIFFUSION, SITTING DROP
7.0
0.1 M malonate, pH 7.0, 12% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
repository
Initial release
Database references
1
0
2013-10-09
1
1
2014-02-19
RCSB
Y
RCSB
2013-08-12
REL
REL
RET
RETINAL
HOH
water
RET
1
2
RET
RET
201
A
HOH
1
3
HOH
HOH
301
A
HOH
2
3
HOH
HOH
302
A
HOH
3
3
HOH
HOH
303
A
HOH
4
3
HOH
HOH
304
A
HOH
5
3
HOH
HOH
305
A
HOH
6
3
HOH
HOH
306
A
HOH
7
3
HOH
HOH
307
A
HOH
8
3
HOH
HOH
308
A
HOH
9
3
HOH
HOH
309
A
PRO
1
n
1
PRO
1
A
ASN
2
n
2
ASN
2
A
PHE
3
n
3
PHE
3
A
SER
4
n
4
SER
4
A
GLY
5
n
5
GLY
5
A
ASN
6
n
6
ASN
6
A
TRP
7
n
7
TRP
7
A
LYS
8
n
8
LYS
8
A
ILE
9
n
9
ILE
9
A
ILE
10
n
10
ILE
10
A
ARG
11
n
11
ARG
11
A
SER
12
n
12
SER
12
A
GLU
13
n
13
GLU
13
A
ASN
14
n
14
ASN
14
A
PHE
15
n
15
PHE
15
A
GLU
16
n
16
GLU
16
A
GLU
17
n
17
GLU
17
A
LEU
18
n
18
LEU
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
VAL
21
n
21
VAL
21
A
LEU
22
n
22
LEU
22
A
GLY
23
n
23
GLY
23
A
VAL
24
n
24
VAL
24
A
ASN
25
n
25
ASN
25
A
VAL
26
n
26
VAL
26
A
MET
27
n
27
MET
27
A
LEU
28
n
28
LEU
28
A
ARG
29
n
29
ARG
29
A
LYS
30
n
30
LYS
30
A
ILE
31
n
31
ILE
31
A
TRP
32
n
32
TRP
32
A
VAL
33
n
33
VAL
33
A
ALA
34
n
34
ALA
34
A
ALA
35
n
35
ALA
35
A
ALA
36
n
36
ALA
36
A
SER
37
n
37
SER
37
A
LYS
38
n
38
LYS
38
A
PRO
39
n
39
PRO
39
A
ALA
40
n
40
ALA
40
A
VAL
41
n
41
VAL
41
A
GLU
42
n
42
GLU
42
A
ILE
43
n
43
ILE
43
A
LYS
44
n
44
LYS
44
A
GLN
45
n
45
GLN
45
A
GLU
46
n
46
GLU
46
A
GLY
47
n
47
GLY
47
A
ASP
48
n
48
ASP
48
A
THR
49
n
49
THR
49
A
PHE
50
n
50
PHE
50
A
TYR
51
n
51
TYR
51
A
ILE
52
n
52
ILE
52
A
LYS
53
n
53
LYS
53
A
VAL
54
n
54
VAL
54
A
SER
55
n
55
SER
55
A
THR
56
n
56
THR
56
A
THR
57
n
57
THR
57
A
VAL
58
n
58
VAL
58
A
TRP
59
n
59
TRP
59
A
THR
60
n
60
THR
60
A
THR
61
n
61
THR
61
A
GLU
62
n
62
GLU
62
A
ILE
63
n
63
ILE
63
A
ASN
64
n
64
ASN
64
A
PHE
65
n
65
PHE
65
A
LYS
66
n
66
LYS
66
A
VAL
67
n
67
VAL
67
A
GLY
68
n
68
GLY
68
A
GLU
69
n
69
GLU
69
A
GLU
70
n
70
GLU
70
A
PHE
71
n
71
PHE
71
A
GLU
72
n
72
GLU
72
A
GLU
73
n
73
GLU
73
A
GLN
74
n
74
GLN
74
A
THR
75
n
75
THR
75
A
VAL
76
n
76
VAL
76
A
ASP
77
n
77
ASP
77
A
GLY
78
n
78
GLY
78
A
ARG
79
n
79
ARG
79
A
PRO
80
n
80
PRO
80
A
CYS
81
n
81
CYS
81
A
LYS
82
n
82
LYS
82
A
SER
83
n
83
SER
83
A
LEU
84
n
84
LEU
84
A
VAL
85
n
85
VAL
85
A
LYS
86
n
86
LYS
86
A
TRP
87
n
87
TRP
87
A
GLU
88
n
88
GLU
88
A
SER
89
n
89
SER
89
A
GLU
90
n
90
GLU
90
A
ASN
91
n
91
ASN
91
A
LYS
92
n
92
LYS
92
A
MET
93
n
93
MET
93
A
VAL
94
n
94
VAL
94
A
CYS
95
n
95
CYS
95
A
GLU
96
n
96
GLU
96
A
GLN
97
n
97
GLN
97
A
LYS
98
n
98
LYS
98
A
LEU
99
n
99
LEU
99
A
LEU
100
n
100
LEU
100
A
LYS
101
n
101
LYS
101
A
GLY
102
n
102
GLY
102
A
GLU
103
n
103
GLU
103
A
GLY
104
n
104
GLY
104
A
PRO
105
n
105
PRO
105
A
LYS
106
n
106
LYS
106
A
THR
107
n
107
THR
107
A
SER
108
n
108
SER
108
A
TRP
109
n
109
TRP
109
A
THR
110
n
110
THR
110
A
LYS
111
n
111
LYS
111
A
GLU
112
n
112
GLU
112
A
LEU
113
n
113
LEU
113
A
THR
114
n
114
THR
114
A
ASN
115
n
115
ASN
115
A
ASP
116
n
116
ASP
116
A
GLY
117
n
117
GLY
117
A
GLU
118
n
118
GLU
118
A
LEU
119
n
119
LEU
119
A
ILE
120
n
120
ILE
120
A
LEU
121
n
121
LEU
121
A
THR
122
n
122
THR
122
A
MET
123
n
123
MET
123
A
THR
124
n
124
THR
124
A
ALA
125
n
125
ALA
125
A
ASP
126
n
126
ASP
126
A
ASP
127
n
127
ASP
127
A
VAL
128
n
128
VAL
128
A
VAL
129
n
129
VAL
129
A
CYS
130
n
130
CYS
130
A
THR
131
n
131
THR
131
A
GLN
132
n
132
GLN
132
A
VAL
133
n
133
VAL
133
A
PHE
134
n
134
PHE
134
A
VAL
135
n
135
VAL
135
A
ARG
136
n
136
ARG
136
A
GLU
137
n
137
GLU
137
A
-0.0465
1.8113
-2.4146
6.4204
-2.7725
3.0910
0.0688
-0.1614
-0.2530
0.2569
-0.4025
-0.4667
-0.2438
0.0892
-0.1391
0.4080
-0.0926
-0.0524
0.3035
0.0361
0.3700
refined
23.6116
-11.8369
-5.1770
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
all
author_defined_assembly
1
monomeric
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
O
PHE
65
A
O
PHE
65
A
N
PHE
50
A
N
PHE
50
A
O
LYS
53
A
O
LYS
53
A
N
GLU
42
A
N
GLU
42
A
O
VAL
41
A
O
VAL
41
A
N
TRP
7
A
N
TRP
7
A
N
GLU
13
A
N
GLU
13
A
O
THR
131
A
O
THR
131
A
O
PHE
134
A
O
PHE
134
A
N
LEU
119
A
N
LEU
119
A
O
ILE
120
A
O
ILE
120
A
N
GLU
112
A
N
GLU
112
A
O
LYS
111
A
O
LYS
111
A
N
MET
93
A
N
MET
93
A
O
VAL
94
A
O
VAL
94
A
N
LYS
86
A
N
LYS
86
A
O
SER
83
A
O
SER
83
A
N
PHE
71
A
N
PHE
71
1
A
CG
GLU
17
A
CG
GLU
17
1
Y
1
A
CD
GLU
17
A
CD
GLU
17
1
Y
1
A
OE1
GLU
17
A
OE1
GLU
17
1
Y
1
A
OE2
GLU
17
A
OE2
GLU
17
1
Y
1
A
CG
LYS
38
A
CG
LYS
38
1
Y
1
A
CD
LYS
38
A
CD
LYS
38
1
Y
1
A
CE
LYS
38
A
CE
LYS
38
1
Y
1
A
NZ
LYS
38
A
NZ
LYS
38
1
Y
1
A
CG
LYS
44
A
CG
LYS
44
1
Y
1
A
CD
LYS
44
A
CD
LYS
44
1
Y
1
A
CE
LYS
44
A
CE
LYS
44
1
Y
1
A
NZ
LYS
44
A
NZ
LYS
44
1
Y
1
A
CG
GLU
46
A
CG
GLU
46
1
Y
1
A
CD
GLU
46
A
CD
GLU
46
1
Y
1
A
OE1
GLU
46
A
OE1
GLU
46
1
Y
1
A
OE2
GLU
46
A
OE2
GLU
46
1
Y
1
A
CG
LYS
66
A
CG
LYS
66
1
Y
1
A
CD
LYS
66
A
CD
LYS
66
1
Y
1
A
CE
LYS
66
A
CE
LYS
66
1
Y
1
A
NZ
LYS
66
A
NZ
LYS
66
1
Y
1
A
CG
GLU
72
A
CG
GLU
72
1
Y
1
A
CD
GLU
72
A
CD
GLU
72
1
Y
1
A
OE1
GLU
72
A
OE1
GLU
72
1
Y
1
A
OE2
GLU
72
A
OE2
GLU
72
1
Y
1
A
CG
LYS
98
A
CG
LYS
98
1
Y
1
A
CD
LYS
98
A
CD
LYS
98
1
Y
1
A
CE
LYS
98
A
CE
LYS
98
1
Y
1
A
NZ
LYS
98
A
NZ
LYS
98
1
Y
1
A
CG
LYS
101
A
CG
LYS
101
1
Y
1
A
CD
LYS
101
A
CD
LYS
101
1
Y
1
A
CE
LYS
101
A
CE
LYS
101
1
Y
1
A
NZ
LYS
101
A
NZ
LYS
101
1
Y
1
A
CG
GLU
103
A
CG
GLU
103
1
Y
1
A
CD
GLU
103
A
CD
GLU
103
1
Y
1
A
OE1
GLU
103
A
OE1
GLU
103
1
Y
1
A
OE2
GLU
103
A
OE2
GLU
103
1
Y
1
A
LYS
38
-118.30
61.25
1
A
THR
56
-94.43
-152.18
1
A
GLU
73
-154.89
-156.65
1
A
ASP
116
-85.29
32.40
1
A
ASP
126
44.80
-108.94
-1.1236
-0.0000
0.0000
-1.1236
-0.0000
2.2472
0.2526
0.2030
0.2054
2.571
44.663
320
6808
4.70
99.44
0.72
1
1.37
MOLECULAR REPLACEMENT
30.46
0.98
1.20
ML
FLAT BULK SOLVENT MODEL
58.926
0.328
2.571
44.663
9
1091
20
0
1062
0.009
1133
1.334
1561
17.126
415
0.082
178
0.008
203
0.3193
0.2604
3.2384
162
3150
99.00
0.2340
0.1892
44.6701
158
3338
100.00
2.528
48.893
4M7M
7211
7165
1
2.528
1
data collection
HKL-2000
phasing
MOLREP
refinement
PHENIX
(phenix.refine: 1.7.2_869)
data reduction
HKL-2000
data scaling
HKL-2000
Cellular retinoic acid-binding protein 2
Crystal structure of the R111K:R132Q:Y134F:T54V:R59W:A32W mutant of the Cellular Retinoic Acid Binding Protein Type II in complex with All-Trans Retinal at 2.57 Angstrom Resolution
1
N
N
2
N
N
3
N
N
A
ASN
14
A
ASN
14
HELX_P
A
GLY
23
A
GLY
23
1
1
10
A
ASN
25
A
ASN
25
HELX_P
A
SER
37
A
SER
37
1
2
13
covale
1.255
doub
A
LYS
111
A
NZ
LYS
111
1_555
A
RET
201
B
C15
RET
1_555
TRANSPORT PROTEIN
protein engineering, wavelength regulation, pH-sensing, Retinylidene PSB, Iminium, TRANSPORT PROTEIN
RABP2_HUMAN
UNP
1
2
P29373
PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRP
CKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE
2
138
4M7M
1
137
P29373
A
1
1
137
1
ALA
ENGINEERED MUTATION
TRP
32
4M7M
A
P29373
UNP
33
32
1
THR
ENGINEERED MUTATION
VAL
54
4M7M
A
P29373
UNP
55
54
1
ARG
ENGINEERED MUTATION
TRP
59
4M7M
A
P29373
UNP
60
59
1
ARG
ENGINEERED MUTATION
LYS
111
4M7M
A
P29373
UNP
112
111
1
ARG
ENGINEERED MUTATION
GLN
132
4M7M
A
P29373
UNP
133
132
1
TYR
ENGINEERED MUTATION
PHE
134
4M7M
A
P29373
UNP
135
134
10
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
60
A
THR
60
A
LYS
66
A
LYS
66
A
THR
49
A
THR
49
A
SER
55
A
SER
55
A
ALA
40
A
ALA
40
A
GLN
45
A
GLN
45
A
GLY
5
A
GLY
5
A
GLU
13
A
GLU
13
A
VAL
128
A
VAL
128
A
ARG
136
A
ARG
136
A
LEU
119
A
LEU
119
A
ALA
125
A
ALA
125
A
THR
107
A
THR
107
A
LEU
113
A
LEU
113
A
LYS
92
A
LYS
92
A
LEU
99
A
LEU
99
A
PRO
80
A
PRO
80
A
TRP
87
A
TRP
87
A
PHE
71
A
PHE
71
A
GLN
74
A
GLN
74
BINDING SITE FOR RESIDUE RET A 201
Software
12
A
PHE
15
A
PHE
15
12
1_555
A
MET
27
A
MET
27
12
5_554
A
TRP
32
A
TRP
32
12
1_555
A
ALA
36
A
ALA
36
12
1_555
A
PRO
39
A
PRO
39
12
1_555
A
ILE
52
A
ILE
52
12
1_555
A
VAL
76
A
VAL
76
12
1_555
A
TRP
109
A
TRP
109
12
1_555
A
LYS
111
A
LYS
111
12
1_555
A
LEU
121
A
LEU
121
12
1_555
A
MET
123
A
MET
123
12
1_555
A
HOH
306
C
HOH
12
1_555
152
P 31 2 1