0.014963
0.008639
0.000000
0.000000
0.017277
0.000000
0.000000
0.000000
0.024422
0.000000
0.000000
0.000000
Ihee, H.
Rajagopal, S.
Srajer, V.
Pahl, R.
Anderson, S.
Schmidt, M.
Schotte, F.
Anfinrud, P.A.
Wulff, M.
Moffat, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
66.833
66.833
40.947
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
US
Proc.Natl.Acad.Sci.Usa
PNASA6
0040
0027-8424
102
7145
7150
10.1073/pnas.0409035102
15870207
Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.
2005
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
288
1
LAUE
L
x-ray
1
1.0
14-ID-B
APS
SYNCHROTRON
APS BEAMLINE 14-ID-B
13888.575
Photoactive yellow protein
1
man
polymer
164.158
4'-HYDROXYCINNAMIC ACID
1
syn
non-polymer
PYP
no
no
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
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
1.90
35.29
VAPOR DIFFUSION, HANGING DROP
7
2.6 M ammonium sulfate, 50 mM sodium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
refine
software
repository
Initial release
Version format compliance
Version format compliance
Other
Refinement description
1
0
2005-07-05
1
1
2008-04-30
1
2
2011-07-13
1
3
2015-09-09
1
4
2017-10-11
_refine.ls_number_reflns_obs
_refine.ls_percent_reflns_obs
_software.name
RCSB
Y
RCSB
2004-06-21
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
GLU
46
n
46
GLU
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
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
TRP
119
A
O
TRP
119
A
N
LYS
110
A
N
LYS
110
A
O
VAL
107
A
O
VAL
107
A
N
PHE
92
A
N
PHE
92
1
-6.68
0.90
118.30
111.62
A
A
A
CB
CG
OD1
ASP
ASP
ASP
65
65
65
N
1
5.88
0.90
118.30
124.18
A
A
A
CB
CG
OD2
ASP
ASP
ASP
65
65
65
N
1
4.30
0.70
120.80
125.10
A
A
A
CB
CG
CD1
PHE
PHE
PHE
75
75
75
N
1
14.53
2.20
113.40
127.93
A
A
A
CA
CB
CG
ASN
ASN
ASN
87
87
87
N
1
-3.81
0.50
120.30
116.49
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
124
124
124
N
2
A
A
C
OXT
VAL
VAL
125
125
0.215
0.019
1.229
1.444
N
1
A
PHE
75
-130.28
-73.62
1
A
ASN
89
-160.33
95.21
1
A
ASP
97
-143.43
16.45
2
A
PHE
75
-125.94
-73.17
2
A
ASP
116
-111.10
62.44
0.3827
0.3526
0.356
0.356
1.6
30
13891
13891
1
0
Difference Fourier
1.6
30
0
987
11
0
976
1.6
30
1TS8
13891
13891
1
100
data reduction
LaueView
refinement
SHELXL-97
data scaling
LaueView
Photoactive yellow protein
Structure of the pR cis planar intermediate from time-resolved Laue crystallography
1
N
N
2
N
N
A
ASP
10
A
ASP
10
HELX_P
A
ALA
16
A
ALA
16
1
1
7
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
1.775
A
CYS
69
A
SG
CYS
69
1_555
A
HC4
169
B
C1
HC4
1_555
photoreceptor
photoreceptor
PYP_ECTHA
UNP
1
1
P16113
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
1
125
1TS8
1
125
P16113
A
1
1
125
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
Software
9
A
TYR
42
A
TYR
42
9
1_555
A
GLU
46
A
GLU
46
9
1_555
A
THR
50
A
THR
50
9
1_555
A
ARG
52
A
ARG
52
9
1_555
A
ALA
67
A
ALA
67
9
1_555
A
PRO
68
A
PRO
68
9
1_555
A
CYS
69
A
CYS
69
9
1_555
A
PHE
96
A
PHE
96
9
1_555
A
TYR
98
A
TYR
98
9
1_555
173
P 63