0.014944
0.008628
0.000000
0.000000
0.017256
0.000000
0.000000
0.000000
0.024389
0.000000
0.000000
0.000000
Rajagopal, S.
Anderson, S.
Srajer, V.
Schmidt, M.
Pahl, R.
Moffat, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
66.917
66.917
41.002
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
C9 H8 O3
164.158
4'-HYDROXYCINNAMIC ACID
PARA-COUMARIC ACID
non-polymer
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
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
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
UK
Structure
STRUE6
2005
0969-2126
13
55
63
10.1016/j.str.2004.10.016
15642261
A Structural Pathway for Signaling in the E46Q Mutant of Photoactive Yellow Protein
2005
10.2210/pdb1t18/pdb
pdb_00001t18
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
288
1
CCD
MARRESEARCH
LAUE
L
x-ray
1
1.0
14-ID-B
APS
SYNCHROTRON
APS BEAMLINE 14-ID-B
13887.591
Photoactive yellow protein
E46Q
1
man
polymer
164.158
4'-HYDROXYCINNAMIC ACID
1
syn
non-polymer
PYP
no
no
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAQGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAQGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
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
Halorhodospira
Escherichia
sample
PYP
1053
Halorhodospira halophila
562
Escherichia coli
1.91
35.54
VAPOR DIFFUSION, HANGING DROP
7
ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
software
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Other
Refinement description
Database references
Derived calculations
1
0
2005-01-18
1
1
2008-04-30
1
2
2011-07-13
1
3
2015-09-09
1
4
2017-10-11
1
5
2021-10-27
_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
RCSB
Y
RCSB
2004-04-15
REL
REL
HC4
4'-HYDROXYCINNAMIC ACID
CYS
69
2
HC4
HC4
169
A
MET
1
n
1
MET
1
A
GLU
2
n
2
GLU
2
A
HIS
3
n
3
HIS
3
A
VAL
4
n
4
VAL
4
A
ALA
5
n
5
ALA
5
A
PHE
6
n
6
PHE
6
A
GLY
7
n
7
GLY
7
A
SER
8
n
8
SER
8
A
GLU
9
n
9
GLU
9
A
ASP
10
n
10
ASP
10
A
ILE
11
n
11
ILE
11
A
GLU
12
n
12
GLU
12
A
ASN
13
n
13
ASN
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
ALA
16
n
16
ALA
16
A
LYS
17
n
17
LYS
17
A
MET
18
n
18
MET
18
A
ASP
19
n
19
ASP
19
A
ASP
20
n
20
ASP
20
A
GLY
21
n
21
GLY
21
A
GLN
22
n
22
GLN
22
A
LEU
23
n
23
LEU
23
A
ASP
24
n
24
ASP
24
A
GLY
25
n
25
GLY
25
A
LEU
26
n
26
LEU
26
A
ALA
27
n
27
ALA
27
A
PHE
28
n
28
PHE
28
A
GLY
29
n
29
GLY
29
A
ALA
30
n
30
ALA
30
A
ILE
31
n
31
ILE
31
A
GLN
32
n
32
GLN
32
A
LEU
33
n
33
LEU
33
A
ASP
34
n
34
ASP
34
A
GLY
35
n
35
GLY
35
A
ASP
36
n
36
ASP
36
A
GLY
37
n
37
GLY
37
A
ASN
38
n
38
ASN
38
A
ILE
39
n
39
ILE
39
A
LEU
40
n
40
LEU
40
A
GLN
41
n
41
GLN
41
A
TYR
42
n
42
TYR
42
A
ASN
43
n
43
ASN
43
A
ALA
44
n
44
ALA
44
A
ALA
45
n
45
ALA
45
A
GLN
46
n
46
GLN
46
A
GLY
47
n
47
GLY
47
A
ASP
48
n
48
ASP
48
A
ILE
49
n
49
ILE
49
A
THR
50
n
50
THR
50
A
GLY
51
n
51
GLY
51
A
ARG
52
n
52
ARG
52
A
ASP
53
n
53
ASP
53
A
PRO
54
n
54
PRO
54
A
LYS
55
n
55
LYS
55
A
GLN
56
n
56
GLN
56
A
VAL
57
n
57
VAL
57
A
ILE
58
n
58
ILE
58
A
GLY
59
n
59
GLY
59
A
LYS
60
n
60
LYS
60
A
ASN
61
n
61
ASN
61
A
PHE
62
n
62
PHE
62
A
PHE
63
n
63
PHE
63
A
LYS
64
n
64
LYS
64
A
ASP
65
n
65
ASP
65
A
VAL
66
n
66
VAL
66
A
ALA
67
n
67
ALA
67
A
PRO
68
n
68
PRO
68
A
CYS
69
n
69
CYS
69
A
THR
70
n
70
THR
70
A
ASP
71
n
71
ASP
71
A
SER
72
n
72
SER
72
A
PRO
73
n
73
PRO
73
A
GLU
74
n
74
GLU
74
A
PHE
75
n
75
PHE
75
A
TYR
76
n
76
TYR
76
A
GLY
77
n
77
GLY
77
A
LYS
78
n
78
LYS
78
A
PHE
79
n
79
PHE
79
A
LYS
80
n
80
LYS
80
A
GLU
81
n
81
GLU
81
A
GLY
82
n
82
GLY
82
A
VAL
83
n
83
VAL
83
A
ALA
84
n
84
ALA
84
A
SER
85
n
85
SER
85
A
GLY
86
n
86
GLY
86
A
ASN
87
n
87
ASN
87
A
LEU
88
n
88
LEU
88
A
ASN
89
n
89
ASN
89
A
THR
90
n
90
THR
90
A
MET
91
n
91
MET
91
A
PHE
92
n
92
PHE
92
A
GLU
93
n
93
GLU
93
A
TYR
94
n
94
TYR
94
A
THR
95
n
95
THR
95
A
PHE
96
n
96
PHE
96
A
ASP
97
n
97
ASP
97
A
TYR
98
n
98
TYR
98
A
GLN
99
n
99
GLN
99
A
MET
100
n
100
MET
100
A
THR
101
n
101
THR
101
A
PRO
102
n
102
PRO
102
A
THR
103
n
103
THR
103
A
LYS
104
n
104
LYS
104
A
VAL
105
n
105
VAL
105
A
LYS
106
n
106
LYS
106
A
VAL
107
n
107
VAL
107
A
HIS
108
n
108
HIS
108
A
MET
109
n
109
MET
109
A
LYS
110
n
110
LYS
110
A
LYS
111
n
111
LYS
111
A
ALA
112
n
112
ALA
112
A
LEU
113
n
113
LEU
113
A
SER
114
n
114
SER
114
A
GLY
115
n
115
GLY
115
A
ASP
116
n
116
ASP
116
A
SER
117
n
117
SER
117
A
TYR
118
n
118
TYR
118
A
TRP
119
n
119
TRP
119
A
VAL
120
n
120
VAL
120
A
PHE
121
n
121
PHE
121
A
VAL
122
n
122
VAL
122
A
LYS
123
n
123
LYS
123
A
ARG
124
n
124
ARG
124
A
VAL
125
n
125
VAL
125
A
0.229
0.2291
0.2401
0.2401
0.2456
0.2456
1671
1682
13.3
13.4
12533
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
LEU
40
A
O
LEU
40
A
N
GLN
32
A
N
GLN
32
A
N
LEU
33
A
N
LEU
33
A
O
TYR
118
A
O
TYR
118
A
O
PHE
121
A
O
PHE
121
A
N
HIS
108
A
N
HIS
108
A
O
VAL
107
A
O
VAL
107
A
N
PHE
92
A
N
PHE
92
2
-6.99
0.90
118.30
111.31
A
A
A
CB
CG
OD1
ASP
ASP
ASP
65
65
65
N
2
6.42
0.90
118.30
124.72
A
A
A
CB
CG
OD2
ASP
ASP
ASP
65
65
65
N
2
-3.71
0.60
121.00
117.29
A
A
A
CB
CG
CD2
TYR
TYR
TYR
76
76
76
N
2
3.85
0.60
121.00
124.85
A
A
A
CB
CG
CD2
TYR
TYR
TYR
94
94
94
N
2
-3.72
0.60
121.00
117.28
A
A
A
CB
CG
CD1
TYR
TYR
TYR
94
94
94
N
2
-10.26
1.60
100.20
89.94
A
A
A
CG
SD
CE
MET
MET
MET
109
109
109
N
2
15.11
2.50
113.10
128.21
A
A
A
N
CA
C
GLY
GLY
GLY
115
115
115
N
2
5.23
0.50
120.30
125.53
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
124
124
124
N
2
-8.07
0.50
120.30
112.23
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
124
124
124
N
1
A
A
C
OXT
VAL
VAL
125
125
0.329
0.019
1.229
1.558
N
1
A
PHE
75
-123.79
-74.18
1
A
ASP
97
-140.69
20.41
1
A
ASP
116
-98.59
55.19
2
A
PHE
75
-130.94
-76.15
2
A
ASN
89
-160.49
97.44
2
A
ASP
97
-143.89
17.21
2
A
ASP
116
-119.63
58.77
0.2468
0.2272
0.229
0.229
1.60
30.00
3953
1306
13889
13889
11012
13.4
100
RANDOM
1
FREE R
0.0
AB INITIO
ENGH AND HUBER
125
0.00
987.00
1.60
30.00
0
987
11
0
976
0.012
0.025
0.000
0.0254
0.062
0.077
0.027
0.000
0.060
0.000
1.6
30
1T18
13957
1
model building
SHELX
refinement
SHELXL-97
data scaling
LaueView
Early intermediate IE1 from time-resolved crystallography of the E46Q mutant of PYP
1
N
N
2
N
N
A
ASP
10
A
ASP
10
HELX_P
A
LEU
15
A
LEU
15
1
1
6
A
ASP
19
A
ASP
19
HELX_P
A
ASP
24
A
ASP
24
1
2
6
A
ASN
43
A
ASN
43
HELX_P
A
GLY
51
A
GLY
51
1
3
9
A
ASP
53
A
ASP
53
HELX_P
A
ILE
58
A
ILE
58
1
4
6
A
ALA
67
A
ALA
67
HELX_P
A
ASP
71
A
ASP
71
5
5
5
A
PHE
75
A
PHE
75
HELX_P
A
GLY
86
A
GLY
86
1
6
12
covale
1.794
one
A
CYS
69
A
SG
CYS
69
1_555
A
HC4
169
B
C1
HC4
1_555
photoreceptor
photoactive yellow protein, PAS domain, photoreceptor
PYP_ECTHA
UNP
1
1
P16113
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
1
125
1T18
1
125
P16113
A
1
1
125
1
GLU
engineered mutation
GLN
46
1T18
A
P16113
UNP
46
46
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
39
A
ILE
39
A
TYR
42
A
TYR
42
A
GLY
29
A
GLY
29
A
ASP
34
A
ASP
34
A
SER
117
A
SER
117
A
ARG
124
A
ARG
124
A
THR
103
A
THR
103
A
LYS
111
A
LYS
111
A
ASN
89
A
ASN
89
A
PHE
96
A
PHE
96
BINDING SITE FOR RESIDUE HC4 A 169
A
HC4
169
Software
9
A
TYR
42
A
TYR
42
9
1_555
A
THR
50
A
THR
50
9
1_555
A
ARG
52
A
ARG
52
9
1_555
A
VAL
66
A
VAL
66
9
1_555
A
ALA
67
A
ALA
67
9
1_555
A
CYS
69
A
CYS
69
9
1_555
A
THR
70
A
THR
70
9
1_555
A
PHE
96
A
PHE
96
9
1_555
A
TYR
98
A
TYR
98
9
1_555
173
P 63