0.036630
0.000000
0.000384
0.000000
0.022272
0.000000
0.000000
0.000000
0.019532
0.00000
0.00000
0.00000
Higuchi, Y.
Yasuoka, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.60
90.00
27.300
44.900
51.200
C3 H7 N O2
89.093
y
ALANINE
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
Fe 3
55.845
FE (III) ION
non-polymer
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 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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
O
N
21
N
N
N
22
N
O
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
N
N
32
S
C
N
33
N
C
N
34
N
O
N
35
N
C
N
36
N
C
N
37
N
O
N
38
N
O
N
39
N
O
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
N
N
48
R
C
N
49
N
C
N
50
N
O
N
51
N
C
N
52
N
S
N
53
N
O
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
FE
N
62
N
N
N
63
S
C
N
64
N
C
N
65
N
O
N
66
N
C
N
67
N
C
N
68
N
C
N
69
N
O
N
70
N
O
N
71
N
O
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
N
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
O
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
O
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
S
C
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
O
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
N
N
117
S
C
N
118
N
C
N
119
N
O
N
120
N
C
N
121
N
C
N
122
N
C
N
123
N
C
N
124
N
N
N
125
N
O
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
N
N
142
S
C
N
143
N
C
N
144
N
O
N
145
N
C
N
146
N
C
N
147
N
S
N
148
N
C
N
149
N
O
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
N
C
Y
166
N
C
Y
167
N
C
Y
168
N
C
Y
169
N
C
Y
170
N
C
Y
171
N
C
N
172
N
O
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
N
N
185
S
C
N
186
N
C
N
187
N
O
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
N
N
202
S
C
N
203
N
C
N
204
N
O
N
205
N
C
N
206
N
O
N
207
N
O
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
N
N
216
S
C
N
217
N
C
N
218
N
O
N
219
R
C
N
220
N
O
N
221
N
C
N
222
N
O
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
N
N
233
S
C
N
234
N
C
N
235
N
O
N
236
N
C
Y
237
N
C
Y
238
N
C
Y
239
N
C
Y
240
N
N
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
N
246
N
O
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
Y
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
Y
269
N
C
N
270
N
O
N
271
N
O
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
N
288
N
C
N
289
N
C
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
doub
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
doub
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
doub
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
doub
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
doub
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
doub
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
Y
161
N
doub
Y
162
N
sing
Y
163
N
sing
N
164
N
sing
Y
165
N
doub
N
166
N
sing
Y
167
N
doub
N
168
N
sing
Y
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
doub
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
doub
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
doub
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
Y
230
N
doub
Y
231
N
sing
Y
232
N
sing
N
233
N
sing
Y
234
N
doub
Y
235
N
sing
Y
236
N
sing
N
237
N
sing
Y
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
Y
258
N
doub
Y
259
N
sing
Y
260
N
sing
N
261
N
sing
Y
262
N
doub
N
263
N
sing
Y
264
N
doub
N
265
N
sing
Y
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
doub
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
55
408
413
10.1107/S0907444998011810
10089348
Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.
1999
NE
Protein Pept.Lett.
PPELEN
2077
0929-8665
5
175
Preliminary Crystallographic Study of Two Crystal Forms of Rubredoxin from Sulfate-Reducing Bactrium
1998
10.2210/pdb2rdv/pdb
pdb_00002rdv
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
IMAGE PLATE
FUJI
SI(111)
M
x-ray
1
1.0
1.0
BL-6A
Photon Factory
1.0
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-6A
5602.237
RUBREDOXIN
3
nat
polymer
55.845
FE (III) ION
3
syn
non-polymer
18.015
water
86
nat
water
no
no
MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA
MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA
A,B,C
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
IAM 12604
Desulfovibrio
sample
883
Desulfovibrio vulgaris str. 'Miyazaki F'
Desulfovibrio vulgaris
MIYAZAKI F
1
1.87
34.2
7.4
pH 7.4
database_2
pdbx_database_status
pdbx_initial_refinement_model
struct_conn
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
Other
Refinement description
Data collection
1
0
1999-05-18
1
1
2008-03-25
1
2
2011-07-13
1
3
2023-08-09
1
4
2024-05-22
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
BNL
1998-10-07
REL
FE
FE (III) ION
HOH
water
1RDV
PDB ENTRY 1RDV
PDB
experimental model
FE
53
2
FE
FE
53
A
FE
53
2
FE
FE
53
B
FE
53
2
FE
FE
53
C
HOH
1
3
HOH
HOH
54
A
HOH
2
3
HOH
HOH
55
A
HOH
3
3
HOH
HOH
56
A
HOH
4
3
HOH
HOH
57
A
HOH
5
3
HOH
HOH
58
A
HOH
6
3
HOH
HOH
59
A
HOH
7
3
HOH
HOH
60
A
HOH
8
3
HOH
HOH
61
A
HOH
9
3
HOH
HOH
62
A
HOH
10
3
HOH
HOH
63
A
HOH
11
3
HOH
HOH
64
A
HOH
12
3
HOH
HOH
65
A
HOH
13
3
HOH
HOH
66
A
HOH
14
3
HOH
HOH
67
A
HOH
15
3
HOH
HOH
68
A
HOH
17
3
HOH
HOH
69
A
HOH
18
3
HOH
HOH
70
A
HOH
19
3
HOH
HOH
71
A
HOH
21
3
HOH
HOH
72
A
HOH
23
3
HOH
HOH
73
A
HOH
24
3
HOH
HOH
74
A
HOH
26
3
HOH
HOH
75
A
HOH
28
3
HOH
HOH
76
A
HOH
30
3
HOH
HOH
77
A
HOH
33
3
HOH
HOH
78
A
HOH
34
3
HOH
HOH
79
A
HOH
65
3
HOH
HOH
80
A
HOH
67
3
HOH
HOH
81
A
HOH
76
3
HOH
HOH
82
A
HOH
79
3
HOH
HOH
83
A
HOH
80
3
HOH
HOH
84
A
HOH
16
3
HOH
HOH
54
B
HOH
29
3
HOH
HOH
55
B
HOH
36
3
HOH
HOH
56
B
HOH
37
3
HOH
HOH
57
B
HOH
39
3
HOH
HOH
58
B
HOH
40
3
HOH
HOH
59
B
HOH
41
3
HOH
HOH
60
B
HOH
42
3
HOH
HOH
61
B
HOH
43
3
HOH
HOH
62
B
HOH
46
3
HOH
HOH
63
B
HOH
47
3
HOH
HOH
64
B
HOH
48
3
HOH
HOH
65
B
HOH
50
3
HOH
HOH
66
B
HOH
52
3
HOH
HOH
67
B
HOH
54
3
HOH
HOH
68
B
HOH
58
3
HOH
HOH
69
B
HOH
82
3
HOH
HOH
70
B
HOH
83
3
HOH
HOH
71
B
HOH
84
3
HOH
HOH
72
B
HOH
86
3
HOH
HOH
73
B
HOH
20
3
HOH
HOH
54
C
HOH
22
3
HOH
HOH
55
C
HOH
25
3
HOH
HOH
56
C
HOH
27
3
HOH
HOH
57
C
HOH
31
3
HOH
HOH
58
C
HOH
32
3
HOH
HOH
59
C
HOH
35
3
HOH
HOH
60
C
HOH
38
3
HOH
HOH
61
C
HOH
44
3
HOH
HOH
62
C
HOH
45
3
HOH
HOH
63
C
HOH
49
3
HOH
HOH
64
C
HOH
51
3
HOH
HOH
65
C
HOH
53
3
HOH
HOH
66
C
HOH
55
3
HOH
HOH
67
C
HOH
56
3
HOH
HOH
68
C
HOH
57
3
HOH
HOH
69
C
HOH
59
3
HOH
HOH
70
C
HOH
60
3
HOH
HOH
71
C
HOH
61
3
HOH
HOH
72
C
HOH
62
3
HOH
HOH
73
C
HOH
63
3
HOH
HOH
74
C
HOH
64
3
HOH
HOH
75
C
HOH
66
3
HOH
HOH
76
C
HOH
68
3
HOH
HOH
77
C
HOH
69
3
HOH
HOH
78
C
HOH
70
3
HOH
HOH
79
C
HOH
71
3
HOH
HOH
80
C
HOH
72
3
HOH
HOH
81
C
HOH
73
3
HOH
HOH
82
C
HOH
74
3
HOH
HOH
83
C
HOH
75
3
HOH
HOH
84
C
HOH
77
3
HOH
HOH
85
C
HOH
78
3
HOH
HOH
86
C
HOH
81
3
HOH
HOH
87
C
HOH
85
3
HOH
HOH
88
C
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
LYS
3
n
3
LYS
3
A
TYR
4
n
4
TYR
4
A
VAL
5
n
5
VAL
5
A
CYS
6
n
6
CYS
6
A
THR
7
n
7
THR
7
A
VAL
8
n
8
VAL
8
A
CYS
9
n
9
CYS
9
A
GLY
10
n
10
GLY
10
A
TYR
11
n
11
TYR
11
A
GLU
12
n
12
GLU
12
A
TYR
13
n
13
TYR
13
A
ASP
14
n
14
ASP
14
A
PRO
15
n
15
PRO
15
A
ALA
16
n
16
ALA
16
A
GLU
17
n
17
GLU
17
A
GLY
18
n
18
GLY
18
A
ASP
19
n
19
ASP
19
A
PRO
20
n
20
PRO
20
A
ASP
21
n
21
ASP
21
A
ASN
22
n
22
ASN
22
A
GLY
23
n
23
GLY
23
A
VAL
24
n
24
VAL
24
A
LYS
25
n
25
LYS
25
A
PRO
26
n
26
PRO
26
A
GLY
27
n
27
GLY
27
A
THR
28
n
28
THR
28
A
ALA
29
n
29
ALA
29
A
PHE
30
n
30
PHE
30
A
GLU
31
n
31
GLU
31
A
ASP
32
n
32
ASP
32
A
VAL
33
n
33
VAL
33
A
PRO
34
n
34
PRO
34
A
ALA
35
n
35
ALA
35
A
ASP
36
n
36
ASP
36
A
TRP
37
n
37
TRP
37
A
VAL
38
n
38
VAL
38
A
CYS
39
n
39
CYS
39
A
PRO
40
n
40
PRO
40
A
ILE
41
n
41
ILE
41
A
CYS
42
n
42
CYS
42
A
GLY
43
n
43
GLY
43
A
ALA
44
n
44
ALA
44
A
PRO
45
n
45
PRO
45
A
LYS
46
n
46
LYS
46
A
SER
47
n
47
SER
47
A
GLU
48
n
48
GLU
48
A
PHE
49
n
49
PHE
49
A
GLU
50
n
50
GLU
50
A
PRO
51
n
51
PRO
51
A
ALA
52
n
52
ALA
52
A
MET
1
n
1
MET
1
B
LYS
2
n
2
LYS
2
B
LYS
3
n
3
LYS
3
B
TYR
4
n
4
TYR
4
B
VAL
5
n
5
VAL
5
B
CYS
6
n
6
CYS
6
B
THR
7
n
7
THR
7
B
VAL
8
n
8
VAL
8
B
CYS
9
n
9
CYS
9
B
GLY
10
n
10
GLY
10
B
TYR
11
n
11
TYR
11
B
GLU
12
n
12
GLU
12
B
TYR
13
n
13
TYR
13
B
ASP
14
n
14
ASP
14
B
PRO
15
n
15
PRO
15
B
ALA
16
n
16
ALA
16
B
GLU
17
n
17
GLU
17
B
GLY
18
n
18
GLY
18
B
ASP
19
n
19
ASP
19
B
PRO
20
n
20
PRO
20
B
ASP
21
n
21
ASP
21
B
ASN
22
n
22
ASN
22
B
GLY
23
n
23
GLY
23
B
VAL
24
n
24
VAL
24
B
LYS
25
n
25
LYS
25
B
PRO
26
n
26
PRO
26
B
GLY
27
n
27
GLY
27
B
THR
28
n
28
THR
28
B
ALA
29
n
29
ALA
29
B
PHE
30
n
30
PHE
30
B
GLU
31
n
31
GLU
31
B
ASP
32
n
32
ASP
32
B
VAL
33
n
33
VAL
33
B
PRO
34
n
34
PRO
34
B
ALA
35
n
35
ALA
35
B
ASP
36
n
36
ASP
36
B
TRP
37
n
37
TRP
37
B
VAL
38
n
38
VAL
38
B
CYS
39
n
39
CYS
39
B
PRO
40
n
40
PRO
40
B
ILE
41
n
41
ILE
41
B
CYS
42
n
42
CYS
42
B
GLY
43
n
43
GLY
43
B
ALA
44
n
44
ALA
44
B
PRO
45
n
45
PRO
45
B
LYS
46
n
46
LYS
46
B
SER
47
n
47
SER
47
B
GLU
48
n
48
GLU
48
B
PHE
49
n
49
PHE
49
B
GLU
50
n
50
GLU
50
B
PRO
51
n
51
PRO
51
B
ALA
52
n
52
ALA
52
B
MET
1
n
1
MET
1
C
LYS
2
n
2
LYS
2
C
LYS
3
n
3
LYS
3
C
TYR
4
n
4
TYR
4
C
VAL
5
n
5
VAL
5
C
CYS
6
n
6
CYS
6
C
THR
7
n
7
THR
7
C
VAL
8
n
8
VAL
8
C
CYS
9
n
9
CYS
9
C
GLY
10
n
10
GLY
10
C
TYR
11
n
11
TYR
11
C
GLU
12
n
12
GLU
12
C
TYR
13
n
13
TYR
13
C
ASP
14
n
14
ASP
14
C
PRO
15
n
15
PRO
15
C
ALA
16
n
16
ALA
16
C
GLU
17
n
17
GLU
17
C
GLY
18
n
18
GLY
18
C
ASP
19
n
19
ASP
19
C
PRO
20
n
20
PRO
20
C
ASP
21
n
21
ASP
21
C
ASN
22
n
22
ASN
22
C
GLY
23
n
23
GLY
23
C
VAL
24
n
24
VAL
24
C
LYS
25
n
25
LYS
25
C
PRO
26
n
26
PRO
26
C
GLY
27
n
27
GLY
27
C
THR
28
n
28
THR
28
C
ALA
29
n
29
ALA
29
C
PHE
30
n
30
PHE
30
C
GLU
31
n
31
GLU
31
C
ASP
32
n
32
ASP
32
C
VAL
33
n
33
VAL
33
C
PRO
34
n
34
PRO
34
C
ALA
35
n
35
ALA
35
C
ASP
36
n
36
ASP
36
C
TRP
37
n
37
TRP
37
C
VAL
38
n
38
VAL
38
C
CYS
39
n
39
CYS
39
C
PRO
40
n
40
PRO
40
C
ILE
41
n
41
ILE
41
C
CYS
42
n
42
CYS
42
C
GLY
43
n
43
GLY
43
C
ALA
44
n
44
ALA
44
C
PRO
45
n
45
PRO
45
C
LYS
46
n
46
LYS
46
C
SER
47
n
47
SER
47
C
GLU
48
n
48
GLU
48
C
PHE
49
n
49
PHE
49
C
GLU
50
n
50
GLU
50
C
PRO
51
n
51
PRO
51
C
ALA
52
n
52
ALA
52
C
author_defined_assembly
1
monomeric
author_defined_assembly
1
monomeric
author_defined_assembly
1
monomeric
A
CYS
6
A
SG
CYS
6
1_555
A
FE
53
D
FE
FE
1_555
A
CYS
9
A
SG
CYS
9
1_555
110.4
A
CYS
6
A
SG
CYS
6
1_555
A
FE
53
D
FE
FE
1_555
A
CYS
39
A
SG
CYS
39
1_555
109.6
A
CYS
9
A
SG
CYS
9
1_555
A
FE
53
D
FE
FE
1_555
A
CYS
39
A
SG
CYS
39
1_555
105.3
A
CYS
6
A
SG
CYS
6
1_555
A
FE
53
D
FE
FE
1_555
A
CYS
42
A
SG
CYS
42
1_555
106.2
A
CYS
9
A
SG
CYS
9
1_555
A
FE
53
D
FE
FE
1_555
A
CYS
42
A
SG
CYS
42
1_555
114.3
A
CYS
39
A
SG
CYS
39
1_555
A
FE
53
D
FE
FE
1_555
A
CYS
42
A
SG
CYS
42
1_555
111.0
B
CYS
6
B
SG
CYS
6
1_555
B
FE
53
E
FE
FE
1_555
B
CYS
9
B
SG
CYS
9
1_555
110.6
B
CYS
6
B
SG
CYS
6
1_555
B
FE
53
E
FE
FE
1_555
B
CYS
39
B
SG
CYS
39
1_555
109.1
B
CYS
9
B
SG
CYS
9
1_555
B
FE
53
E
FE
FE
1_555
B
CYS
39
B
SG
CYS
39
1_555
105.8
B
CYS
6
B
SG
CYS
6
1_555
B
FE
53
E
FE
FE
1_555
B
CYS
42
B
SG
CYS
42
1_555
106.3
B
CYS
9
B
SG
CYS
9
1_555
B
FE
53
E
FE
FE
1_555
B
CYS
42
B
SG
CYS
42
1_555
113.9
B
CYS
39
B
SG
CYS
39
1_555
B
FE
53
E
FE
FE
1_555
B
CYS
42
B
SG
CYS
42
1_555
111.1
C
CYS
6
C
SG
CYS
6
1_555
C
FE
53
F
FE
FE
1_555
C
CYS
9
C
SG
CYS
9
1_555
112.7
C
CYS
6
C
SG
CYS
6
1_555
C
FE
53
F
FE
FE
1_555
C
CYS
39
C
SG
CYS
39
1_555
109.5
C
CYS
9
C
SG
CYS
9
1_555
C
FE
53
F
FE
FE
1_555
C
CYS
39
C
SG
CYS
39
1_555
106.4
C
CYS
6
C
SG
CYS
6
1_555
C
FE
53
F
FE
FE
1_555
C
CYS
42
C
SG
CYS
42
1_555
106.0
C
CYS
9
C
SG
CYS
9
1_555
C
FE
53
F
FE
FE
1_555
C
CYS
42
C
SG
CYS
42
1_555
112.3
C
CYS
39
C
SG
CYS
39
1_555
C
FE
53
F
FE
FE
1_555
C
CYS
42
C
SG
CYS
42
1_555
109.9
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
VAL
5
A
O
VAL
5
A
N
GLU
50
A
N
GLU
50
B
O
VAL
5
B
O
VAL
5
B
N
GLU
50
B
N
GLU
50
C
O
LYS
3
C
O
LYS
3
C
N
ALA
52
C
N
ALA
52
1
A
A
O
O
HOH
HOH
65
77
2.15
1
C
C
O
O
HOH
HOH
85
88
2.18
1
A
ASP
19
-158.21
74.75
1
B
PRO
34
-38.52
136.46
14.1
0.2160000
0.1750000
0.1750000
1.9
20.0
9604
5
82.5
RANDOM
1
RESTRAINED
3.0
MOLECULAR REPLACEMENT
PDB ENTRY 1RDV
1.9
20.0
86
1262
3
0
1173
0.012
1.807
1.633
1.9
20.0
2RDV
53316
0.0
0.1110000
1
82.5
model building
X-PLOR
refinement
X-PLOR
data reduction
WEIS
data scaling
FSCALE
phasing
X-PLOR
RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
3
N
N
A
PRO
20
A
PRO
20
HELX_P
A
ASN
22
A
ASN
22
5
1
3
A
PHE
30
A
PHE
30
HELX_P
A
ASP
32
A
ASP
32
5
2
3
A
LYS
46
A
LYS
46
HELX_P
A
GLU
48
A
GLU
48
5
3
3
B
PRO
20
B
PRO
20
HELX_P
B
ASN
22
B
ASN
22
5
4
3
B
PHE
30
B
PHE
30
HELX_P
B
ASP
32
B
ASP
32
5
5
3
B
LYS
46
B
LYS
46
HELX_P
B
GLU
48
B
GLU
48
5
6
3
C
PRO
20
C
PRO
20
HELX_P
C
ASN
22
C
ASN
22
5
7
3
C
PHE
30
C
PHE
30
HELX_P
C
ASP
32
C
ASP
32
5
8
3
C
LYS
46
C
LYS
46
HELX_P
C
GLU
48
C
GLU
48
5
9
3
metalc
2.304
A
CYS
6
A
SG
CYS
6
1_555
A
FE
53
D
FE
FE
1_555
metalc
2.317
A
CYS
9
A
SG
CYS
9
1_555
A
FE
53
D
FE
FE
1_555
metalc
2.291
A
CYS
39
A
SG
CYS
39
1_555
A
FE
53
D
FE
FE
1_555
metalc
2.320
A
CYS
42
A
SG
CYS
42
1_555
A
FE
53
D
FE
FE
1_555
metalc
2.321
B
CYS
6
B
SG
CYS
6
1_555
B
FE
53
E
FE
FE
1_555
metalc
2.321
B
CYS
9
B
SG
CYS
9
1_555
B
FE
53
E
FE
FE
1_555
metalc
2.294
B
CYS
39
B
SG
CYS
39
1_555
B
FE
53
E
FE
FE
1_555
metalc
2.313
B
CYS
42
B
SG
CYS
42
1_555
B
FE
53
E
FE
FE
1_555
metalc
2.320
C
CYS
6
C
SG
CYS
6
1_555
C
FE
53
F
FE
FE
1_555
metalc
2.313
C
CYS
9
C
SG
CYS
9
1_555
C
FE
53
F
FE
FE
1_555
metalc
2.314
C
CYS
39
C
SG
CYS
39
1_555
C
FE
53
F
FE
FE
1_555
metalc
2.293
C
CYS
42
C
SG
CYS
42
1_555
C
FE
53
F
FE
FE
1_555
ELECTRON TRANSFER
RUBREDOXIN, COMPND, ELECTRON TRANSFER PROTEIN, METALLOPROTEIN, SULFATE-REDUCING BACTERIUM, ELECTRON TRANSFER
given
-0.541000
0.840000
0.023000
-0.840000
-0.542000
0.027000
0.036000
-0.005000
0.999000
8.02800
3.19800
-34.31000
given
-0.502000
-0.864000
-0.030000
0.864000
-0.503000
0.007000
-0.021000
-0.022000
1.000000
8.87000
-5.09600
-16.95300
RUBR_DESVM
UNP
1
1
P15412
MKKYVCTVCGYEYDPAEGDPDNGVKPGTAFEDVPADWVCPICGAPKSEFEPA
1
52
2RDV
1
52
P15412
A
1
1
52
1
52
2RDV
1
52
P15412
B
1
1
52
1
52
2RDV
1
52
P15412
C
1
1
52
2
2
2
anti-parallel
anti-parallel
anti-parallel
A
TYR
4
A
TYR
4
A
CYS
6
A
CYS
6
A
PHE
49
A
PHE
49
A
PRO
51
A
PRO
51
B
TYR
4
B
TYR
4
B
CYS
6
B
CYS
6
B
PHE
49
B
PHE
49
B
PRO
51
B
PRO
51
C
LYS
3
C
LYS
3
C
CYS
6
C
CYS
6
C
PHE
49
C
PHE
49
C
ALA
52
C
ALA
52
FE COORDINATION SITE, CHAIN A.
Unknown
4
FE COORDINATION SITE, CHAIN B.
Unknown
4
FE COORDINATION SITE, CHAIN C.
Unknown
4
BINDING SITE FOR RESIDUE FE A 53
A
FE
53
Software
4
BINDING SITE FOR RESIDUE FE B 53
B
FE
53
Software
4
BINDING SITE FOR RESIDUE FE C 53
C
FE
53
Software
4
A
CYS
6
A
CYS
6
4
1_555
A
CYS
9
A
CYS
9
4
1_555
A
CYS
39
A
CYS
39
4
1_555
A
CYS
42
A
CYS
42
4
1_555
B
CYS
6
B
CYS
6
4
1_555
B
CYS
9
B
CYS
9
4
1_555
B
CYS
39
B
CYS
39
4
1_555
B
CYS
42
B
CYS
42
4
1_555
C
CYS
6
C
CYS
6
4
1_555
C
CYS
9
C
CYS
9
4
1_555
C
CYS
39
C
CYS
39
4
1_555
C
CYS
42
C
CYS
42
4
1_555
A
CYS
6
A
CYS
6
4
1_555
A
CYS
9
A
CYS
9
4
1_555
A
CYS
39
A
CYS
39
4
1_555
A
CYS
42
A
CYS
42
4
1_555
B
CYS
6
B
CYS
6
4
1_555
B
CYS
9
B
CYS
9
4
1_555
B
CYS
39
B
CYS
39
4
1_555
B
CYS
42
B
CYS
42
4
1_555
C
CYS
6
C
CYS
6
4
1_555
C
CYS
9
C
CYS
9
4
1_555
C
CYS
39
C
CYS
39
4
1_555
C
CYS
42
C
CYS
42
4
1_555
4
P 1 21 1