0.014963
0.008639
0.000000
0.000000
0.017277
0.000000
0.000000
0.000000
0.024422
0.00000
0.00000
0.00000
Schotte, F.
Cho, H.S.
Kaila, V.R.I.
Kamikubo, H.
Dashdorj, N.
Henry, E.R.
Graber, T.J.
Henning, R.
Wulff, M.
Hummer, G.
Kataoka, M.
Anfinrud, P.A.
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
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
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
109
19256
10.1073/PNAS.1210938109
23132943
Watching a Signaling Protein Function in Real Time Via 100-Ps Time-Resolved Laue Crystallography.
2012
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
MIRRORS
CCD
2011-03-12
RAYONIX SX-165mm
LAUE
L
x-ray
1
0.96
1.0
1.30
1.0
14-ID-B
APS
0.96-1.30
SYNCHROTRON
APS BEAMLINE 14-ID-B
13888.575
PHOTOACTIVE YELLOW PROTEIN
1
man
polymer
164.158
4'-HYDROXYCINNAMIC ACID
1
syn
non-polymer
18.015
water
140
nat
water
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
sample
1053
HALORHODOSPIRA HALOPHILA
469008
ESCHERICHIA COLI
BL21(DE3)
PLASMID
PET16B
3
1.9
35.24
NONE
VAPOR DIFFUSION, HANGING DROP
9.0
2.2 M AMMONIUM SULFATE, 1.0 M SODIUM CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM DEUTERIUM PHOSPHATE, PH 9.0, VAPOUR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE 295 K
295
database_PDB_rev
database_PDB_rev_record
exptl_crystal_grow
repository
Initial release
Database references
Data collection
Data collection
Experimental preparation
1
0
2012-11-14
1
1
2012-12-05
1
2
2017-01-25
1
3
2019-01-30
_exptl_crystal_grow.method
_exptl_crystal_grow.temp
CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVEYELLOW PROTEIN
CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANTT50V
CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANTY42F
CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN
CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G51S MUTANT
CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G47S/G51S MUTANT
CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEINRECONSTITUTED WITH CAFFEIC ACID AT 1.16 A RESOLUTION
PYP ULTRA-HIGH RESOLUTION STRUCTURE OF A BACTERIALPHOTORECEPTOR
PHOTOACTIVE YELLOW PROTEIN 1-25 DELETION MUTANT
CRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OFPHOTOACTIVE YELLOW PROTEIN UNDER CONTINUOUS ILLUMINATIONAT 110K
CRYOTRAPPED STATE IN WILD TYPE PHOTOACTIVE YELLOW PROTEIN,INDUCED WITH CONTINUOUS ILLUMINATION AT 110K
E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K
WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K
STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN ANDTHEIR ROLE IN ITS PHOTOCYCLE
E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 110K
E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 295K
PHOTOACTIVATED CHROMOPHORE CONFORMATION IN PHOTOACTIVEYELLOW PROTEIN (E46Q MUTANT) FROM 10 MICROSECONDS TO 3MILLISECONDS
PHOTOACTIVATED CHROMOPHORE CONFORMATION IN PHOTOACTIVEYELLOW PROTEIN (E46Q MUTANT) FROM 10 TO 500 NANOSECONDS
STRUCTURE OF A REACTION INTERMEDIATE IN THE PHOTOCYCLE OFPYP EXTRACTED BY A SVD-DRIVEN ANALYSIS
REACTION INTERMEDIATE IN THE PHOTOCYCLE OF PYP, INTERMEDIATE OCCUPIED BETWEEN 100 MICRO-SECONDS TO 5 MILLI-SECONDS
EARLY INTERMEDIATE IE1 FROM TIME-RESOLVED CRYSTALLOGRAPHYOF THE E46Q MUTANT OF PYP
EARLY INTERMEDIATE IE2 FROM TIME-RESOLVED CRYSTALLOGRAPHYOF THE E46Q MUTANT OF PYP
LATE INTERMEDIATE IL1 FROM TIME-RESOLVED CRYSTALLOGRAPHY OFTHE E46Q MUTANT OF PYP
LATE INTERMEDIATE IL2 FROM TIME-RESOLVED CRYSTALLOGRAPHY OFTHE E46Q MUTANT OF PYP
LATE INTERMEDIATE IL3 FROM TIME-RESOLVED CRYSTALLOGRAPHY OFTHE E46Q MUTANT OF PYP
STRUCTURE OF THE PB1 INTERMEDIATE FROM TIME-RESOLVED LAUECRYSTALLOGRAPHY
STRUCTURE OF THE PB2 INTERMEDIATE FROM TIME-RESOLVED LAUECRYSTALLOGRAPHY
STRUCTURE OF THE PR CIS WOBBLE AND PR E46Q INTERMEDIATESFROM TIME-RESOLVED LAUE CRYSTALLOGRAPHY
STRUCTURE OF THE PR CIS PLANAR INTERMEDIATE FROM TIME -RESOLVED LAUE CRYSTALLOGRAPHY
CRYSTAL STRUCTURE OF PYP E46Q MUTANT
THE INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN: A COMMON MECHANISM ON LIGHT ACTIVATION IN PHOTORECEPTOR PROTEINS
INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN
NMR STRUCTURE OF THE GROUND STATE OF THE PHOTOACTIVE YELLOWPROTEIN LACKING THE N-TERMINAL PART
STRUCTURE OF THE BLUE SHIFTED INTERMEDIATE STATE OF THEPHOTOACTIVE YELLOW PROTEIN LACKING THE N-TERMINAL PART
WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P65 FORM
R52Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 FORM
PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED) 2PHY 3
PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50% GROUND STATE, 50% BLEACHED
PHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K)
PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES
PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLEINTERMEDIATE
THE PR0 PHOTOCYCLE INTERMEDIATE OF PHOTOACTIVE YELLOW PROTEIN
THE PR1 PHOTOCYCLE INTERMEDIATE OF PHOTOACTIVE YELLOW PROTEIN
THE PR1 PHOTOCYCLE INTERMEDIATE OF PHOTOACTIVE YELLOW PROTEIN
PDBE
Y
PDBE
2012-09-28
REL
1
A
O
HOH
2014
6.50
1
A
O
HOH
2040
6.10
1
A
O
HOH
2051
6.68
HC4
4'-HYDROXYCINNAMIC ACID
HOH
water
HC4
169
2
HC4
HC4
169
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2044
3
HOH
HOH
2044
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2046
3
HOH
HOH
2046
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2049
3
HOH
HOH
2049
A
HOH
2050
3
HOH
HOH
2050
A
HOH
2051
3
HOH
HOH
2051
A
HOH
2052
3
HOH
HOH
2052
A
HOH
2053
3
HOH
HOH
2053
A
HOH
2054
3
HOH
HOH
2054
A
HOH
2055
3
HOH
HOH
2055
A
HOH
2056
3
HOH
HOH
2056
A
HOH
2057
3
HOH
HOH
2057
A
HOH
2058
3
HOH
HOH
2058
A
HOH
2059
3
HOH
HOH
2059
A
HOH
2060
3
HOH
HOH
2060
A
HOH
2061
3
HOH
HOH
2061
A
HOH
2062
3
HOH
HOH
2062
A
HOH
2063
3
HOH
HOH
2063
A
HOH
2064
3
HOH
HOH
2064
A
HOH
2065
3
HOH
HOH
2065
A
HOH
2066
3
HOH
HOH
2066
A
HOH
2067
3
HOH
HOH
2067
A
HOH
2068
3
HOH
HOH
2068
A
HOH
2069
3
HOH
HOH
2069
A
HOH
2070
3
HOH
HOH
2070
A
HOH
2071
3
HOH
HOH
2071
A
HOH
2072
3
HOH
HOH
2072
A
HOH
2073
3
HOH
HOH
2073
A
HOH
2074
3
HOH
HOH
2074
A
HOH
2075
3
HOH
HOH
2075
A
HOH
2076
3
HOH
HOH
2076
A
HOH
2077
3
HOH
HOH
2077
A
HOH
2078
3
HOH
HOH
2078
A
HOH
2079
3
HOH
HOH
2079
A
HOH
2080
3
HOH
HOH
2080
A
HOH
2081
3
HOH
HOH
2081
A
HOH
2082
3
HOH
HOH
2082
A
HOH
2083
3
HOH
HOH
2083
A
HOH
2084
3
HOH
HOH
2084
A
HOH
2085
3
HOH
HOH
2085
A
HOH
2086
3
HOH
HOH
2086
A
HOH
2087
3
HOH
HOH
2087
A
HOH
2088
3
HOH
HOH
2088
A
HOH
2089
3
HOH
HOH
2089
A
HOH
2090
3
HOH
HOH
2090
A
HOH
2091
3
HOH
HOH
2091
A
HOH
2092
3
HOH
HOH
2092
A
HOH
2093
3
HOH
HOH
2093
A
HOH
2094
3
HOH
HOH
2094
A
HOH
2095
3
HOH
HOH
2095
A
HOH
2096
3
HOH
HOH
2096
A
HOH
2097
3
HOH
HOH
2097
A
HOH
2098
3
HOH
HOH
2098
A
HOH
2099
3
HOH
HOH
2099
A
HOH
2100
3
HOH
HOH
2100
A
HOH
2101
3
HOH
HOH
2101
A
HOH
2102
3
HOH
HOH
2102
A
HOH
2103
3
HOH
HOH
2103
A
HOH
2104
3
HOH
HOH
2104
A
HOH
2105
3
HOH
HOH
2105
A
HOH
2106
3
HOH
HOH
2106
A
HOH
2107
3
HOH
HOH
2107
A
HOH
2108
3
HOH
HOH
2108
A
HOH
2109
3
HOH
HOH
2109
A
HOH
2110
3
HOH
HOH
2110
A
HOH
2111
3
HOH
HOH
2111
A
HOH
2112
3
HOH
HOH
2112
A
HOH
2113
3
HOH
HOH
2113
A
HOH
2114
3
HOH
HOH
2114
A
HOH
2115
3
HOH
HOH
2115
A
HOH
2116
3
HOH
HOH
2116
A
HOH
2117
3
HOH
HOH
2117
A
HOH
2118
3
HOH
HOH
2118
A
HOH
2119
3
HOH
HOH
2119
A
HOH
2120
3
HOH
HOH
2120
A
HOH
2121
3
HOH
HOH
2121
A
HOH
2122
3
HOH
HOH
2122
A
HOH
2123
3
HOH
HOH
2123
A
HOH
2124
3
HOH
HOH
2124
A
HOH
2125
3
HOH
HOH
2125
A
HOH
2126
3
HOH
HOH
2126
A
HOH
2127
3
HOH
HOH
2127
A
HOH
2128
3
HOH
HOH
2128
A
HOH
2129
3
HOH
HOH
2129
A
HOH
2130
3
HOH
HOH
2130
A
HOH
2131
3
HOH
HOH
2131
A
HOH
2132
3
HOH
HOH
2132
A
HOH
2133
3
HOH
HOH
2133
A
HOH
2134
3
HOH
HOH
2134
A
HOH
2135
3
HOH
HOH
2135
A
HOH
2136
3
HOH
HOH
2136
A
HOH
2137
3
HOH
HOH
2137
A
HOH
2138
3
HOH
HOH
2138
A
HOH
2139
3
HOH
HOH
2139
A
HOH
2140
3
HOH
HOH
2140
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_and_software_defined_assembly
PISA
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
40
A
O
GLN
32
A
O
GLN
32
A
N
LEU
33
A
N
LEU
33
A
O
TYR
118
A
O
TYR
118
A
N
LYS
123
A
N
LYS
123
A
O
LYS
106
A
O
LYS
106
A
N
MET
109
A
N
MET
109
A
O
THR
90
A
O
THR
90
1
A
A
O
O
HOH
HOH
2035
2055
1.79
1
A
A
O
O
HOH
HOH
2081
2083
1.82
1
A
A
O
O
HOH
HOH
2062
2063
1.93
1
A
A
OH
O
TYR
HOH
98
2116
1.95
1
A
A
O
O
HOH
HOH
2112
2114
1.97
1
A
A
O
O
HOH
HOH
2004
2006
2.01
1
A
A
O
O
HOH
HOH
2068
2072
2.04
1
A
A
O
O
HOH
HOH
2069
2083
2.05
1
A
A
OE1
O
GLN
HOH
99
2118
2.07
1
A
A
O
O
HOH
HOH
2016
2017
2.09
1
A
A
O
O
HOH
HOH
2065
2117
2.10
1
A
A
O
O
HOH
HOH
2020
2022
2.12
1
A
A
NH1
O
ARG
HOH
52
2068
2.18
1
A
A
OE1
O
GLU
HOH
9
2017
2.19
1
A
A
O
O
HOH
HOH
2038
2121
1.99
1_555
3_555
1
A
A
O
O
HOH
HOH
2059
2100
2.08
1_555
6_555
1
A
A
O
O
HOH
HOH
2051
2051
2.18
1_555
3_555
1
A
A
NZ
O
LYS
HOH
55
2099
2.18
1_555
6_555
1
A
PHE
75
-128.83
-72.70
1
A
ASP
116
-141.74
45.82
22.7
0.4098
0.0000
0.0000
0.4098
0.0000
-0.8197
0.3600
0.2551
0.2593
1.600
13.285
382
9409
4.1
67.86
0.61
1
0.00
OTHER
43.59
0.00
0.00
NONE
ML
FLAT BULK SOLVENT MODEL
6.812
0.126
1.600
13.285
140
1127
11
0
976
0.007
1009
1.179
1359
16.674
367
0.081
140
0.005
180
0.5333
0.4270
1.8313
80
2145
49.00
0.3775
0.3097
2.3053
151
3352
76.00
0.3241
0.2028
13.2851
151
3530
79.00
12.88
1.60
13.28
4BBV
10605
2.0
0.20
1
5.10
5.1
50.0
0.15
1.60
1.70
0.60
1
2.6
13.0
refinement
PHENIX
(PHENIX.REFINE)
data reduction
d*TREK
data scaling
d*TREK
PHOTOACTIVE YELLOW PROTEIN
The PB0 Photocycle Intermediate of Photoactive Yellow Protein
1
N
N
2
N
N
3
N
N
A
ASP
10
A
ASP
10
HELX_P
A
LYS
17
A
LYS
17
1
1
8
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
PHE
62
A
PHE
62
HELX_P
A
VAL
66
A
VAL
66
1
5
5
A
ALA
67
A
ALA
67
HELX_P
A
ASP
71
A
ASP
71
5
6
5
A
PHE
75
A
PHE
75
HELX_P
A
GLY
86
A
GLY
86
1
7
12
covale
1.757
A
HC4
169
B
C1
HC4
1_555
A
CYS
69
A
SG
CYS
69
1_555
SIGNALING PROTEIN
PHOTORECEPTOR, LIGHT SENSOR, CHROMOPHORE, PHOTORECEPTOR PROTEIN, RECEPTOR, SENSORY TRANSDUCTION, SIGNALING PROTEIN, PAS, LOV
PYP_HALHA
UNP
1
P16113
1
125
4BBV
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
10
A
THR
50
A
THR
50
10
1_555
A
ARG
52
A
ARG
52
10
1_555
A
VAL
66
A
VAL
66
10
1_555
A
ALA
67
A
ALA
67
10
1_555
A
PRO
68
A
PRO
68
10
1_555
A
CYS
69
A
CYS
69
10
1_555
A
THR
70
A
THR
70
10
1_555
A
PHE
96
A
PHE
96
10
1_555
A
TYR
98
A
TYR
98
10
1_555
A
HOH
2115
C
HOH
10
1_555
173
P 63