0.024654
0.014234
0.000000
0.000000
0.028468
0.000000
0.000000
0.000000
0.008468
0.000000
0.000000
0.000000
Van Aalten, D.M.F.
Crielaard, W.
Hellingwerf, K.J.
Joshua-Tor, L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
40.561
40.561
118.089
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
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
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
Protein Sci.
PRCIEI
0795
0961-8368
9
64
72
10739248
Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.
2000
US
Biochemistry
BICHAW
0033
0006-2960
34
6278
6287
1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore.
1995
US
Biochemistry
BICHAW
0033
0006-2960
37
12689
12699
10.1021/bi9806652
Solution structure and backbone dynamics of the photoactive yellow protein.
1998
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
IMAGE PLATE
1998-02-01
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.08
1.0
X26C
NSLS
1.08
SYNCHROTRON
NSLS BEAMLINE X26C
13490.118
PHOTOACTIVE YELLOW PROTEIN
1
man
polymer
164.158
4'-HYDROXYCINNAMIC ACID
1
syn
non-polymer
18.015
water
151
nat
water
PYP
no
no
VAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGV
ASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
VAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGV
ASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
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
Halorhodospira
Escherichia
sample
1053
Halorhodospira halophila
562
Escherichia coli
M15
PLASMID
PHISP
1
2.02
39.0
VAPOR DIFFUSION, HANGING DROP
6.5
PEG 2K, MES., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 17K
290.0
pdbx_unobs_or_zero_occ_atoms
software
exptl_crystal_grow
repository
Initial release
Version format compliance
Version format compliance
Advisory
Refinement description
Experimental preparation
1
0
2000-03-31
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2018-01-31
_software.classification
_software.name
_exptl_crystal_grow.temp
P63 CRYSTAL FORM, USED FOR MR
RCSB
Y
RCSB
1999-10-17
REL
HC4
4'-HYDROXYCINNAMIC ACID
HOH
water
HC4
126
2
HC4
HC4
126
A
HOH
1001
3
HOH
HOH
1001
A
HOH
1002
3
HOH
HOH
1002
A
HOH
1003
3
HOH
HOH
1003
A
HOH
1004
3
HOH
HOH
1004
A
HOH
1005
3
HOH
HOH
1005
A
HOH
1006
3
HOH
HOH
1006
A
HOH
1007
3
HOH
HOH
1007
A
HOH
1008
3
HOH
HOH
1008
A
HOH
1009
3
HOH
HOH
1009
A
HOH
1010
3
HOH
HOH
1010
A
HOH
1011
3
HOH
HOH
1011
A
HOH
1012
3
HOH
HOH
1012
A
HOH
1013
3
HOH
HOH
1013
A
HOH
1014
3
HOH
HOH
1014
A
HOH
1015
3
HOH
HOH
1015
A
HOH
1016
3
HOH
HOH
1016
A
HOH
1017
3
HOH
HOH
1017
A
HOH
1018
3
HOH
HOH
1018
A
HOH
1019
3
HOH
HOH
1019
A
HOH
1020
3
HOH
HOH
1020
A
HOH
1021
3
HOH
HOH
1021
A
HOH
1022
3
HOH
HOH
1022
A
HOH
1023
3
HOH
HOH
1023
A
HOH
1024
3
HOH
HOH
1024
A
HOH
1025
3
HOH
HOH
1025
A
HOH
1026
3
HOH
HOH
1026
A
HOH
1027
3
HOH
HOH
1027
A
HOH
1028
3
HOH
HOH
1028
A
HOH
1029
3
HOH
HOH
1029
A
HOH
1030
3
HOH
HOH
1030
A
HOH
1031
3
HOH
HOH
1031
A
HOH
1032
3
HOH
HOH
1032
A
HOH
1033
3
HOH
HOH
1033
A
HOH
1034
3
HOH
HOH
1034
A
HOH
1035
3
HOH
HOH
1035
A
HOH
1036
3
HOH
HOH
1036
A
HOH
1037
3
HOH
HOH
1037
A
HOH
1038
3
HOH
HOH
1038
A
HOH
1039
3
HOH
HOH
1039
A
HOH
1040
3
HOH
HOH
1040
A
HOH
1041
3
HOH
HOH
1041
A
HOH
1042
3
HOH
HOH
1042
A
HOH
1043
3
HOH
HOH
1043
A
HOH
1044
3
HOH
HOH
1044
A
HOH
1045
3
HOH
HOH
1045
A
HOH
1046
3
HOH
HOH
1046
A
HOH
1047
3
HOH
HOH
1047
A
HOH
1048
3
HOH
HOH
1048
A
HOH
1049
3
HOH
HOH
1049
A
HOH
1050
3
HOH
HOH
1050
A
HOH
1051
3
HOH
HOH
1051
A
HOH
1052
3
HOH
HOH
1052
A
HOH
1053
3
HOH
HOH
1053
A
HOH
1054
3
HOH
HOH
1054
A
HOH
1055
3
HOH
HOH
1055
A
HOH
1056
3
HOH
HOH
1056
A
HOH
1057
3
HOH
HOH
1057
A
HOH
1058
3
HOH
HOH
1058
A
HOH
1059
3
HOH
HOH
1059
A
HOH
1060
3
HOH
HOH
1060
A
HOH
1061
3
HOH
HOH
1061
A
HOH
1062
3
HOH
HOH
1062
A
HOH
1063
3
HOH
HOH
1063
A
HOH
1064
3
HOH
HOH
1064
A
HOH
1065
3
HOH
HOH
1065
A
HOH
1066
3
HOH
HOH
1066
A
HOH
1067
3
HOH
HOH
1067
A
HOH
1068
3
HOH
HOH
1068
A
HOH
1069
3
HOH
HOH
1069
A
HOH
1070
3
HOH
HOH
1070
A
HOH
1071
3
HOH
HOH
1071
A
HOH
1072
3
HOH
HOH
1072
A
HOH
1073
3
HOH
HOH
1073
A
HOH
1074
3
HOH
HOH
1074
A
HOH
1075
3
HOH
HOH
1075
A
HOH
1076
3
HOH
HOH
1076
A
HOH
1077
3
HOH
HOH
1077
A
HOH
1078
3
HOH
HOH
1078
A
HOH
1079
3
HOH
HOH
1079
A
HOH
1080
3
HOH
HOH
1080
A
HOH
1081
3
HOH
HOH
1081
A
HOH
1082
3
HOH
HOH
1082
A
HOH
1083
3
HOH
HOH
1083
A
HOH
1084
3
HOH
HOH
1084
A
HOH
1085
3
HOH
HOH
1085
A
HOH
1086
3
HOH
HOH
1086
A
HOH
1087
3
HOH
HOH
1087
A
HOH
1088
3
HOH
HOH
1088
A
HOH
1089
3
HOH
HOH
1089
A
HOH
1090
3
HOH
HOH
1090
A
HOH
1091
3
HOH
HOH
1091
A
HOH
1092
3
HOH
HOH
1092
A
HOH
1093
3
HOH
HOH
1093
A
HOH
1094
3
HOH
HOH
1094
A
HOH
1095
3
HOH
HOH
1095
A
HOH
1096
3
HOH
HOH
1096
A
HOH
1097
3
HOH
HOH
1097
A
HOH
1098
3
HOH
HOH
1098
A
HOH
1099
3
HOH
HOH
1099
A
HOH
1100
3
HOH
HOH
1100
A
HOH
1101
3
HOH
HOH
1101
A
HOH
1102
3
HOH
HOH
1102
A
HOH
1103
3
HOH
HOH
1103
A
HOH
1104
3
HOH
HOH
1104
A
HOH
1105
3
HOH
HOH
1105
A
HOH
1106
3
HOH
HOH
1106
A
HOH
1107
3
HOH
HOH
1107
A
HOH
1108
3
HOH
HOH
1108
A
HOH
1109
3
HOH
HOH
1109
A
HOH
1110
3
HOH
HOH
1110
A
HOH
1111
3
HOH
HOH
1111
A
HOH
1112
3
HOH
HOH
1112
A
HOH
1113
3
HOH
HOH
1113
A
HOH
1114
3
HOH
HOH
1114
A
HOH
1115
3
HOH
HOH
1115
A
HOH
1116
3
HOH
HOH
1116
A
HOH
1117
3
HOH
HOH
1117
A
HOH
1118
3
HOH
HOH
1118
A
HOH
1119
3
HOH
HOH
1119
A
HOH
1120
3
HOH
HOH
1120
A
HOH
1121
3
HOH
HOH
1121
A
HOH
1122
3
HOH
HOH
1122
A
HOH
1123
3
HOH
HOH
1123
A
HOH
1124
3
HOH
HOH
1124
A
HOH
1125
3
HOH
HOH
1125
A
HOH
1126
3
HOH
HOH
1126
A
HOH
1127
3
HOH
HOH
1127
A
HOH
1128
3
HOH
HOH
1128
A
HOH
1129
3
HOH
HOH
1129
A
HOH
1130
3
HOH
HOH
1130
A
HOH
1131
3
HOH
HOH
1131
A
HOH
1132
3
HOH
HOH
1132
A
HOH
1133
3
HOH
HOH
1133
A
HOH
1134
3
HOH
HOH
1134
A
HOH
1135
3
HOH
HOH
1135
A
HOH
1136
3
HOH
HOH
1136
A
HOH
1137
3
HOH
HOH
1137
A
HOH
1138
3
HOH
HOH
1138
A
HOH
1139
3
HOH
HOH
1139
A
HOH
1140
3
HOH
HOH
1140
A
HOH
1141
3
HOH
HOH
1141
A
HOH
1142
3
HOH
HOH
1142
A
HOH
1143
3
HOH
HOH
1143
A
HOH
1144
3
HOH
HOH
1144
A
HOH
1145
3
HOH
HOH
1145
A
HOH
1146
3
HOH
HOH
1146
A
HOH
1147
3
HOH
HOH
1147
A
HOH
1148
3
HOH
HOH
1148
A
HOH
1149
3
HOH
HOH
1149
A
HOH
1150
3
HOH
HOH
1150
A
HOH
1151
3
HOH
HOH
1151
A
VAL
4
n
1
VAL
4
A
ALA
5
n
2
ALA
5
A
PHE
6
n
3
PHE
6
A
GLY
7
n
4
GLY
7
A
SER
8
n
5
SER
8
A
GLU
9
n
6
GLU
9
A
ASP
10
n
7
ASP
10
A
ILE
11
n
8
ILE
11
A
GLU
12
n
9
GLU
12
A
ASN
13
n
10
ASN
13
A
THR
14
n
11
THR
14
A
LEU
15
n
12
LEU
15
A
ALA
16
n
13
ALA
16
A
LYS
17
n
14
LYS
17
A
MET
18
n
15
MET
18
A
ASP
19
n
16
ASP
19
A
ASP
20
n
17
ASP
20
A
GLY
21
n
18
GLY
21
A
GLN
22
n
19
GLN
22
A
LEU
23
n
20
LEU
23
A
ASP
24
n
21
ASP
24
A
GLY
25
n
22
GLY
25
A
LEU
26
n
23
LEU
26
A
ALA
27
n
24
ALA
27
A
PHE
28
n
25
PHE
28
A
GLY
29
n
26
GLY
29
A
ALA
30
n
27
ALA
30
A
ILE
31
n
28
ILE
31
A
GLN
32
n
29
GLN
32
A
LEU
33
n
30
LEU
33
A
ASP
34
n
31
ASP
34
A
GLY
35
n
32
GLY
35
A
ASP
36
n
33
ASP
36
A
GLY
37
n
34
GLY
37
A
ASN
38
n
35
ASN
38
A
ILE
39
n
36
ILE
39
A
LEU
40
n
37
LEU
40
A
GLN
41
n
38
GLN
41
A
TYR
42
n
39
TYR
42
A
ASN
43
n
40
ASN
43
A
ALA
44
n
41
ALA
44
A
ALA
45
n
42
ALA
45
A
GLU
46
n
43
GLU
46
A
GLY
47
n
44
GLY
47
A
ASP
48
n
45
ASP
48
A
ILE
49
n
46
ILE
49
A
THR
50
n
47
THR
50
A
GLY
51
n
48
GLY
51
A
ARG
52
n
49
ARG
52
A
ASP
53
n
50
ASP
53
A
PRO
54
n
51
PRO
54
A
LYS
55
n
52
LYS
55
A
GLN
56
n
53
GLN
56
A
VAL
57
n
54
VAL
57
A
ILE
58
n
55
ILE
58
A
GLY
59
n
56
GLY
59
A
LYS
60
n
57
LYS
60
A
ASN
61
n
58
ASN
61
A
PHE
62
n
59
PHE
62
A
PHE
63
n
60
PHE
63
A
LYS
64
n
61
LYS
64
A
ASP
65
n
62
ASP
65
A
VAL
66
n
63
VAL
66
A
ALA
67
n
64
ALA
67
A
PRO
68
n
65
PRO
68
A
CYS
69
n
66
CYS
69
A
THR
70
n
67
THR
70
A
ASP
71
n
68
ASP
71
A
SER
72
n
69
SER
72
A
PRO
73
n
70
PRO
73
A
GLU
74
n
71
GLU
74
A
PHE
75
n
72
PHE
75
A
TYR
76
n
73
TYR
76
A
GLY
77
n
74
GLY
77
A
LYS
78
n
75
LYS
78
A
PHE
79
n
76
PHE
79
A
LYS
80
n
77
LYS
80
A
GLU
81
n
78
GLU
81
A
GLY
82
n
79
GLY
82
A
VAL
83
n
80
VAL
83
A
ALA
84
n
81
ALA
84
A
SER
85
n
82
SER
85
A
GLY
86
n
83
GLY
86
A
ASN
87
n
84
ASN
87
A
LEU
88
n
85
LEU
88
A
ASN
89
n
86
ASN
89
A
THR
90
n
87
THR
90
A
MET
91
n
88
MET
91
A
PHE
92
n
89
PHE
92
A
GLU
93
n
90
GLU
93
A
TYR
94
n
91
TYR
94
A
THR
95
n
92
THR
95
A
PHE
96
n
93
PHE
96
A
ASP
97
n
94
ASP
97
A
TYR
98
n
95
TYR
98
A
GLN
99
n
96
GLN
99
A
MET
100
n
97
MET
100
A
THR
101
n
98
THR
101
A
PRO
102
n
99
PRO
102
A
THR
103
n
100
THR
103
A
LYS
104
n
101
LYS
104
A
VAL
105
n
102
VAL
105
A
LYS
106
n
103
LYS
106
A
VAL
107
n
104
VAL
107
A
HIS
108
n
105
HIS
108
A
MET
109
n
106
MET
109
A
LYS
110
n
107
LYS
110
A
LYS
111
n
108
LYS
111
A
ALA
112
n
109
ALA
112
A
LEU
113
n
110
LEU
113
A
n
111
114
A
n
112
115
A
ASP
116
n
113
ASP
116
A
SER
117
n
114
SER
117
A
TYR
118
n
115
TYR
118
A
TRP
119
n
116
TRP
119
A
VAL
120
n
117
VAL
120
A
PHE
121
n
118
PHE
121
A
VAL
122
n
119
VAL
122
A
LYS
123
n
120
LYS
123
A
ARG
124
n
121
ARG
124
A
VAL
125
n
122
VAL
125
A
0.1380000
0.1950000
5.0
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
N
LEU
40
A
N
LEU
37
A
O
GLN
32
A
O
GLN
29
A
N
LEU
33
A
N
LEU
30
A
O
TYR
118
A
O
TYR
115
A
O
LYS
123
A
O
LYS
120
A
N
LYS
106
A
N
LYS
103
A
N
MET
109
A
N
MET
106
A
O
THR
90
A
O
THR
87
1
A
N
ASP
116
A
N
ASP
113
1
Y
1
A
CA
ASP
116
A
CA
ASP
113
1
Y
1
A
CB
ASP
116
A
CB
ASP
113
1
Y
1
A
CG
ASP
116
A
CG
ASP
113
1
Y
1
A
OD1
ASP
116
A
OD1
ASP
113
1
Y
1
A
OD2
ASP
116
A
OD2
ASP
113
1
Y
1
A
SER
114
A
SER
111
1
Y
1
A
GLY
115
A
GLY
112
1
Y
1
-15.82
1.40
112.40
96.58
A
A
A
CA
CB
CG2
THR
THR
THR
50
50
50
B
B
N
1
3.74
0.50
120.30
124.04
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
124
124
124
N
1
-3.47
0.50
120.30
116.83
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
124
124
124
N
1
A
PHE
75
-128.49
-82.69
1
A
ASN
89
-169.30
92.89
1
A
ASP
97
-147.34
17.37
0.1980000
0.1390000
0.1390000
1.39
8.0
1041
20594
20594
5.0
100
RANDOM
1
0.0
ENGH & HUBER (IN SHELX)
1.39
8.0
211
1164
11
0
942
0.008
1.92
15.9
1.39
15.0
1D7E
194171
194171
-3.0
0.0390000
1
23.1
8.9
98.8
0.1260000
1.39
1.44
100.0
phasing
AMoRE
refinement
SHELXL-97
data collection
MAR345
data scaling
SCALEPACK
PHOTOACTIVE YELLOW PROTEIN
CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN
1
N
N
2
N
N
3
N
N
A
ASP
10
A
ASP
7
HELX_P
A
LYS
17
A
LYS
14
1
1
8
A
ASP
19
A
ASP
16
HELX_P
A
GLY
25
A
GLY
22
1
2
7
A
ASN
43
A
ASN
40
HELX_P
A
GLY
51
A
GLY
48
1
3
9
A
ASP
53
A
ASP
50
HELX_P
A
ILE
58
A
ILE
55
1
4
6
A
ALA
67
A
ALA
64
HELX_P
A
ASP
71
A
ASP
68
5
5
5
A
PHE
75
A
PHE
72
HELX_P
A
GLY
86
A
GLY
83
1
6
12
covale
1.737
A
CYS
69
A
SG
CYS
66
1_555
A
HC4
126
B
C1
HC4
1_555
PHOTOSYNTHESIS
PHOTORECEPTOR, PHOTOSYNTHESIS
PYP_ECTHA
UNP
1
P16113
4
125
1D7E
4
125
P16113
A
1
1
122
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
39
A
ILE
36
A
TYR
42
A
TYR
39
A
GLY
29
A
GLY
26
A
LEU
33
A
LEU
30
A
TYR
118
A
TYR
115
A
ARG
124
A
ARG
121
A
THR
103
A
THR
100
A
LYS
111
A
LYS
108
A
ASN
89
A
ASN
86
A
PHE
96
A
PHE
93
BINDING SITE FOR RESIDUE HC4 A 126
Software
12
A
ILE
31
A
ILE
28
12
1_555
A
TYR
42
A
TYR
39
12
1_555
A
GLU
46
A
GLU
43
12
1_555
A
THR
50
A
THR
47
12
1_555
A
ARG
52
A
ARG
49
12
1_555
A
PHE
62
A
PHE
59
12
1_555
A
VAL
66
A
VAL
63
12
1_555
A
ALA
67
A
ALA
64
12
1_555
A
PRO
68
A
PRO
65
12
1_555
A
CYS
69
A
CYS
66
12
1_555
A
PHE
96
A
PHE
93
12
1_555
A
TYR
98
A
TYR
95
12
1_555
170
P 65