0.016404
0.009471
0.000000
0.000000
0.018942
0.000000
0.000000
0.000000
0.009093
0.00000
0.00000
0.00000
Royant, A.
Edman, K.
Ursby, T.
Pebay-Peyroula, E.
Landau, E.M.
Neutze, R.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
60.960
60.960
109.970
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
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
UK
Nature
NATUAS
0006
0028-0836
406
645
10.1038/35020599
10949307
Helix Deformation is Coupled to Vectorial Proton Transport in Bacteriorhodopsin'S Photocycle
2000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
110.0
1
CCD
1999-10-15
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.934
1.0
ID14-1
ESRF
0.934
SYNCHROTRON
ESRF BEAMLINE ID14-1
CONFORMER B IS GROUND STATE, CONFORMER A IS THE L-STATE FORM.
24990.535
BACTERIORHODOPSIN, GROUND STATE
1
nat
polymer
284.436
RETINAL
1
syn
non-polymer
18.015
water
30
nat
water
no
no
TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYA
DWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMR
PEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE
TGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYWARYA
DWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKAESMR
PEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGE
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
2242
HALOBACTERIUM SALINARIUM
S9
1
2.36
48
5.60
PROTEIN FROM THE PURPLE MEMBRANE WAS RESOLVED IN OCTYL GLUC, pH 5.60
repository
Initial release
Version format compliance
Version format compliance
1
0
2000-08-19
1
1
2011-05-08
1
2
2011-07-13
X-RAY STRUCTURE OF BACTERIORHODOPSIN GROWN IN LIPIDIC CUBIC PHASES
HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE
PDBE
Y
PDBE
2000-04-04
REL
RET
RETINAL
HOH
water
ALTERNATE CONFORMER B GROUND STATE MODEL FROM 1QHJ
ALTERNATE CONFORMER A L-STATE MODEL
RET
300
2
RET
RET
300
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
THR
5
n
1
THR
5
A
GLY
6
n
2
GLY
6
A
ARG
7
n
3
ARG
7
A
PRO
8
n
4
PRO
8
A
GLU
9
n
5
GLU
9
A
TRP
10
n
6
TRP
10
A
ILE
11
n
7
ILE
11
A
TRP
12
n
8
TRP
12
A
LEU
13
n
9
LEU
13
A
ALA
14
n
10
ALA
14
A
LEU
15
n
11
LEU
15
A
GLY
16
n
12
GLY
16
A
THR
17
n
13
THR
17
A
ALA
18
n
14
ALA
18
A
LEU
19
n
15
LEU
19
A
MET
20
n
16
MET
20
A
GLY
21
n
17
GLY
21
A
LEU
22
n
18
LEU
22
A
GLY
23
n
19
GLY
23
A
THR
24
n
20
THR
24
A
LEU
25
n
21
LEU
25
A
TYR
26
n
22
TYR
26
A
PHE
27
n
23
PHE
27
A
LEU
28
n
24
LEU
28
A
VAL
29
n
25
VAL
29
A
LYS
30
n
26
LYS
30
A
GLY
31
n
27
GLY
31
A
MET
32
n
28
MET
32
A
GLY
33
n
29
GLY
33
A
VAL
34
n
30
VAL
34
A
SER
35
n
31
SER
35
A
ASP
36
n
32
ASP
36
A
PRO
37
n
33
PRO
37
A
ASP
38
n
34
ASP
38
A
ALA
39
n
35
ALA
39
A
LYS
40
n
36
LYS
40
A
LYS
41
n
37
LYS
41
A
PHE
42
n
38
PHE
42
A
TYR
43
n
39
TYR
43
A
ALA
44
n
40
ALA
44
A
ILE
45
n
41
ILE
45
A
THR
46
n
42
THR
46
A
THR
47
n
43
THR
47
A
LEU
48
n
44
LEU
48
A
VAL
49
n
45
VAL
49
A
PRO
50
n
46
PRO
50
A
ALA
51
n
47
ALA
51
A
ILE
52
n
48
ILE
52
A
ALA
53
n
49
ALA
53
A
PHE
54
n
50
PHE
54
A
THR
55
n
51
THR
55
A
MET
56
n
52
MET
56
A
TYR
57
n
53
TYR
57
A
LEU
58
n
54
LEU
58
A
SER
59
n
55
SER
59
A
MET
60
n
56
MET
60
A
LEU
61
n
57
LEU
61
A
LEU
62
n
58
LEU
62
A
GLY
63
n
59
GLY
63
A
TYR
64
n
60
TYR
64
A
GLY
65
n
61
GLY
65
A
LEU
66
n
62
LEU
66
A
THR
67
n
63
THR
67
A
MET
68
n
64
MET
68
A
VAL
69
n
65
VAL
69
A
PRO
70
n
66
PRO
70
A
PHE
71
n
67
PHE
71
A
GLY
72
n
68
GLY
72
A
GLY
73
n
69
GLY
73
A
GLU
74
n
70
GLU
74
A
GLN
75
n
71
GLN
75
A
ASN
76
n
72
ASN
76
A
PRO
77
n
73
PRO
77
A
ILE
78
n
74
ILE
78
A
TYR
79
n
75
TYR
79
A
TRP
80
n
76
TRP
80
A
ALA
81
n
77
ALA
81
A
ARG
82
n
78
ARG
82
A
TYR
83
n
79
TYR
83
A
ALA
84
n
80
ALA
84
A
ASP
85
n
81
ASP
85
A
TRP
86
n
82
TRP
86
A
LEU
87
n
83
LEU
87
A
PHE
88
n
84
PHE
88
A
THR
89
n
85
THR
89
A
THR
90
n
86
THR
90
A
PRO
91
n
87
PRO
91
A
LEU
92
n
88
LEU
92
A
LEU
93
n
89
LEU
93
A
LEU
94
n
90
LEU
94
A
LEU
95
n
91
LEU
95
A
ASP
96
n
92
ASP
96
A
LEU
97
n
93
LEU
97
A
ALA
98
n
94
ALA
98
A
LEU
99
n
95
LEU
99
A
LEU
100
n
96
LEU
100
A
VAL
101
n
97
VAL
101
A
ASP
102
n
98
ASP
102
A
ALA
103
n
99
ALA
103
A
ASP
104
n
100
ASP
104
A
GLN
105
n
101
GLN
105
A
GLY
106
n
102
GLY
106
A
THR
107
n
103
THR
107
A
ILE
108
n
104
ILE
108
A
LEU
109
n
105
LEU
109
A
ALA
110
n
106
ALA
110
A
LEU
111
n
107
LEU
111
A
VAL
112
n
108
VAL
112
A
GLY
113
n
109
GLY
113
A
ALA
114
n
110
ALA
114
A
ASP
115
n
111
ASP
115
A
GLY
116
n
112
GLY
116
A
ILE
117
n
113
ILE
117
A
MET
118
n
114
MET
118
A
ILE
119
n
115
ILE
119
A
GLY
120
n
116
GLY
120
A
THR
121
n
117
THR
121
A
GLY
122
n
118
GLY
122
A
LEU
123
n
119
LEU
123
A
VAL
124
n
120
VAL
124
A
GLY
125
n
121
GLY
125
A
ALA
126
n
122
ALA
126
A
LEU
127
n
123
LEU
127
A
THR
128
n
124
THR
128
A
LYS
129
n
125
LYS
129
A
VAL
130
n
126
VAL
130
A
TYR
131
n
127
TYR
131
A
SER
132
n
128
SER
132
A
TYR
133
n
129
TYR
133
A
ARG
134
n
130
ARG
134
A
PHE
135
n
131
PHE
135
A
VAL
136
n
132
VAL
136
A
TRP
137
n
133
TRP
137
A
TRP
138
n
134
TRP
138
A
ALA
139
n
135
ALA
139
A
ILE
140
n
136
ILE
140
A
SER
141
n
137
SER
141
A
THR
142
n
138
THR
142
A
ALA
143
n
139
ALA
143
A
ALA
144
n
140
ALA
144
A
MET
145
n
141
MET
145
A
LEU
146
n
142
LEU
146
A
TYR
147
n
143
TYR
147
A
ILE
148
n
144
ILE
148
A
LEU
149
n
145
LEU
149
A
TYR
150
n
146
TYR
150
A
VAL
151
n
147
VAL
151
A
LEU
152
n
148
LEU
152
A
PHE
153
n
149
PHE
153
A
PHE
154
n
150
PHE
154
A
GLY
155
n
151
GLY
155
A
PHE
156
n
152
PHE
156
A
THR
157
n
153
THR
157
A
SER
158
n
154
SER
158
A
LYS
159
n
155
LYS
159
A
ALA
160
n
156
ALA
160
A
GLU
161
n
157
GLU
161
A
SER
162
n
158
SER
162
A
MET
163
n
159
MET
163
A
ARG
164
n
160
ARG
164
A
PRO
165
n
161
PRO
165
A
GLU
166
n
162
GLU
166
A
VAL
167
n
163
VAL
167
A
ALA
168
n
164
ALA
168
A
SER
169
n
165
SER
169
A
THR
170
n
166
THR
170
A
PHE
171
n
167
PHE
171
A
LYS
172
n
168
LYS
172
A
VAL
173
n
169
VAL
173
A
LEU
174
n
170
LEU
174
A
ARG
175
n
171
ARG
175
A
ASN
176
n
172
ASN
176
A
VAL
177
n
173
VAL
177
A
THR
178
n
174
THR
178
A
VAL
179
n
175
VAL
179
A
VAL
180
n
176
VAL
180
A
LEU
181
n
177
LEU
181
A
TRP
182
n
178
TRP
182
A
SER
183
n
179
SER
183
A
ALA
184
n
180
ALA
184
A
TYR
185
n
181
TYR
185
A
PRO
186
n
182
PRO
186
A
VAL
187
n
183
VAL
187
A
VAL
188
n
184
VAL
188
A
TRP
189
n
185
TRP
189
A
LEU
190
n
186
LEU
190
A
ILE
191
n
187
ILE
191
A
GLY
192
n
188
GLY
192
A
SER
193
n
189
SER
193
A
GLU
194
n
190
GLU
194
A
GLY
195
n
191
GLY
195
A
ALA
196
n
192
ALA
196
A
GLY
197
n
193
GLY
197
A
ILE
198
n
194
ILE
198
A
VAL
199
n
195
VAL
199
A
PRO
200
n
196
PRO
200
A
LEU
201
n
197
LEU
201
A
ASN
202
n
198
ASN
202
A
ILE
203
n
199
ILE
203
A
GLU
204
n
200
GLU
204
A
THR
205
n
201
THR
205
A
LEU
206
n
202
LEU
206
A
LEU
207
n
203
LEU
207
A
PHE
208
n
204
PHE
208
A
MET
209
n
205
MET
209
A
VAL
210
n
206
VAL
210
A
LEU
211
n
207
LEU
211
A
ASP
212
n
208
ASP
212
A
VAL
213
n
209
VAL
213
A
SER
214
n
210
SER
214
A
ALA
215
n
211
ALA
215
A
LYS
216
n
212
LYS
216
A
VAL
217
n
213
VAL
217
A
GLY
218
n
214
GLY
218
A
PHE
219
n
215
PHE
219
A
GLY
220
n
216
GLY
220
A
LEU
221
n
217
LEU
221
A
ILE
222
n
218
ILE
222
A
LEU
223
n
219
LEU
223
A
LEU
224
n
220
LEU
224
A
ARG
225
n
221
ARG
225
A
SER
226
n
222
SER
226
A
ARG
227
n
223
ARG
227
A
ALA
228
n
224
ALA
228
A
ILE
229
n
225
ILE
229
A
PHE
230
n
226
PHE
230
A
GLY
231
n
227
GLY
231
A
GLU
232
n
228
GLU
232
A
author_and_software_defined_assembly
PISA
3
trimeric
6230
-50.93
26190
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
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_565
-x+y,-x+1,z
crystal symmetry operation
-30.4800000000
52.7929086147
0.0000000000
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_665
-y+1,x-y+1,z
crystal symmetry operation
30.4800000000
52.7929086147
0.0000000000
A
N
PHE
71
A
N
PHE
67
A
O
GLU
74
A
O
GLU
70
1
A
CG
MET
163
A
CG
MET
159
1
Y
1
A
SD
MET
163
A
SD
MET
159
1
Y
1
A
CE
MET
163
A
CE
MET
159
1
Y
1
A
CG
ARG
227
A
CG
ARG
223
1
Y
1
A
CD
ARG
227
A
CD
ARG
223
1
Y
1
A
NE
ARG
227
A
NE
ARG
223
1
Y
1
A
CZ
ARG
227
A
CZ
ARG
223
1
Y
1
A
NH1
ARG
227
A
NH1
ARG
223
1
Y
1
A
NH2
ARG
227
A
NH2
ARG
223
1
Y
1
A
CG
GLU
232
A
CG
GLU
228
1
Y
1
A
CD
GLU
232
A
CD
GLU
228
1
Y
1
A
OE1
GLU
232
A
OE1
GLU
228
1
Y
1
A
OE2
GLU
232
A
OE2
GLU
228
1
Y
1
A
ARG
7
B
-155.47
-71.22
1
A
PHE
71
B
-177.53
149.62
1
A
PHE
156
A
-129.32
-61.80
1
A
PHE
156
B
-127.29
-64.70
1
A
LYS
216
B
-107.55
-62.53
1
A
VAL
217
A
-122.08
-56.19
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
RETFIN-CIS.PAR
RETFIN.TOP
40.0
-3.96
-0.40
0.00
-3.96
0.00
7.91
THE COORDINATE FILE CONTAINS 2 MODELS CHAINS A AND B, ONLY A WAS REFINED, B WAS FIXED DURING THE WHOLE REFINEMENT. THE NUMBER OF ATOMS USED IN THE REFINEMENT REFERES TO CHAIN A. FREE R VALUE TEST SET SAME AS PREVIOUS REFINEMENTS 1QHJ, 1QKP, 1QKO
0.288
0.012
0.265
0.265
2.1
30.5
593
12912
4.6
95.4
RANDOM
2443186
1
RESTRAINED
THROUGHOUT
0.0
OTHER
FLAT MODEL
75.56
0.404
0.35
0.32
5.00
0.23
0.31
2.1
30.5
30
1802
20
0
1752
0.008
1.1
18.7
0.77
0.286
0.031
0.289
2.23
87
2111
6
4.0
98.9
19.4
2.100
30.500
1E0P
13088
0.06300
1
9.0000
5.600
96.6
2.10
2.21
1.400
0.52100
1
5.80
99.2
refinement
CNS
1.0
data reduction
DENZO
data scaling
SCALA
data scaling
SCALEPACK
phasing
CNS
1.0
BACTERIORHODOPSIN, GROUND STATE
L intermediate of bacteriorhodopsin
1
N
N
2
N
N
3
N
N
A
GLU
9
A
GLU
5
HELX_P
A
GLY
31
A
GLY
27
1
1
23
A
MET
32
A
MET
28
HELX_P
A
VAL
34
A
VAL
30
5
2
3
A
ASP
36
A
ASP
32
HELX_P
A
LEU
62
A
LEU
58
1
3
27
A
TYR
79
A
TYR
75
HELX_P
A
ASP
102
A
ASP
98
1
4
24
A
ASP
104
A
ASP
100
HELX_P
A
THR
128
A
THR
124
1
5
25
A
VAL
130
A
VAL
126
HELX_P
A
GLY
155
A
GLY
151
1
6
26
A
PHE
156
A
PHE
152
HELX_P
A
GLU
161
A
GLU
157
1
7
6
A
ARG
164
A
ARG
160
HELX_P
A
GLY
192
A
GLY
188
1
8
29
A
PRO
200
A
PRO
196
HELX_P
A
VAL
217
A
VAL
213
1
9
18
A
VAL
217
A
VAL
213
HELX_P
A
LEU
224
A
LEU
220
1
10
8
A
ARG
225
A
ARG
221
HELX_P
A
PHE
230
A
PHE
226
5
11
6
covale
1.308
B
B
A
LYS
216
A
NZ
LYS
212
1_555
A
RET
300
B
C15
RET
1_555
covale
1.283
A
A
A
LYS
216
A
NZ
LYS
212
1_555
A
RET
300
B
C15
RET
1_555
TRANSPORT
TRANSPORT, ION TRANSPORT, PHOTORECEPTOR, TRANSMEMBRANE, RETINAL PROTEIN HYDROGEN ION TRANSPORT
BACR_HALHA
UNP
1
P02945
18
245
1E0P
5
232
P02945
A
1
1
228
2
anti-parallel
A
THR
67
A
THR
63
A
PHE
71
A
PHE
67
A
GLU
74
A
GLU
70
A
ILE
78
A
ILE
74
BINDING SITE FOR RESIDUE RET A 300
Software
16
A
TRP
86
A
TRP
82
16
1_555
A
THR
89
A
THR
85
16
1_555
A
THR
90
A
THR
86
16
1_555
A
LEU
93
A
LEU
89
16
1_555
A
MET
118
A
MET
114
16
1_555
A
GLY
122
A
GLY
118
16
1_555
A
TRP
138
A
TRP
134
16
1_555
A
SER
141
A
SER
137
16
1_555
A
THR
142
A
THR
138
16
1_555
A
TRP
182
A
TRP
178
16
1_555
A
TYR
185
A
TYR
181
16
1_555
A
PRO
186
A
PRO
182
16
1_555
A
TRP
189
A
TRP
185
16
1_555
A
ASP
212
A
ASP
208
16
1_555
A
ALA
215
A
ALA
211
16
1_555
A
LYS
216
A
LYS
212
16
1_555
173
P 63